Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet: Optimization of CometChip (A and B) Representative pictures of “comet” of ring and schizont-stage P. falciparum 3D7 after on-chip hydrogen peroxide (H 2 O 2 ) treatment. Each green dot indicates a microwell in the CometChip. Each macrowell of the 96-well plate contains around ~300 of such microwells. The magnified view of the boxed area below shows the differentiation of head (between the green line and red line) and tail (between the red line and blue line) of an individual comet. This process would be automatically done by the algorithm as shown in the . Scale bars, 50 nm. (C) Quantification of “comet” after treatment. The y axis represents the percentage of DNA at the “comet” tail (%Tail DNA). On average, ~306 comets were analyzed per macrowell. Each experiment was done in technical triplicates, and data here were collected and are shown in biological triplicates. ∗ p < 0.05; ∗∗ p < 0.01, one-way analysis of variance (ANOVA). Dunnett’s multiple comparison tests were performed between vehicle control (0 μM) and respective concentrations. All data are indicated as means ± SEM.

Article Snippet: CometChip raw data and analyzed results, Part four , This paper; Mendeley data , https://doi.org/10.17632/dwcv62mrbn.1.

Techniques: Comparison, Control

Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet: Artesunate-Induced DNA Damage in P. falciparum Lab Strains (A) Schematic illustration of artesunate treatment based on Streptolysin O (SLO) enrichment (ring stage) or Percoll gradient centrifugation (schizont stage). (B) Artesunate-induced DNA damage in P. falciparum 3D7, Dd2, and Dd2 I543T . Ring-stage (upper panel) and schizont-stage (lower panel) P. falciparum parasites were treated with different concentrations of artesunate for 1 h and subjected to analysis on alkaline CometChip. On average, ~302 comets were analyzed per macrowell. Each experiment was done in technical triplicates, and data here were collected and are shown in biological triplicates or quadruplicates. ∗∗ p < 0.01; ∗∗∗ p < 0.001; ∗∗∗∗ p < 0.0001, one-way ANOVA. Dunnett’s multiple comparison tests were performed between vehicle control (0 μM) and respective concentrations. All data are indicated as means ± SEM.

Article Snippet: CometChip raw data and analyzed results, Part four , This paper; Mendeley data , https://doi.org/10.17632/dwcv62mrbn.1.

Techniques: Gradient Centrifugation, Comparison, Control

Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet:

Article Snippet: CometChip raw data and analyzed results, Part four , This paper; Mendeley data , https://doi.org/10.17632/dwcv62mrbn.1.

Techniques: Recombinant, Giemsa Stain, Saline, Purification, Plasmid Preparation, Software

Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet: Optimization of CometChip (A and B) Representative pictures of “comet” of ring and schizont-stage P. falciparum 3D7 after on-chip hydrogen peroxide (H 2 O 2 ) treatment. Each green dot indicates a microwell in the CometChip. Each macrowell of the 96-well plate contains around ~300 of such microwells. The magnified view of the boxed area below shows the differentiation of head (between the green line and red line) and tail (between the red line and blue line) of an individual comet. This process would be automatically done by the algorithm as shown in the . Scale bars, 50 nm. (C) Quantification of “comet” after treatment. The y axis represents the percentage of DNA at the “comet” tail (%Tail DNA). On average, ~306 comets were analyzed per macrowell. Each experiment was done in technical triplicates, and data here were collected and are shown in biological triplicates. ∗ p < 0.05; ∗∗ p < 0.01, one-way analysis of variance (ANOVA). Dunnett’s multiple comparison tests were performed between vehicle control (0 μM) and respective concentrations. All data are indicated as means ± SEM.

Article Snippet: CometChip raw data and analyzed results, Part six , This paper; Mendeley data , https://doi.org/10.17632/grdkg7rb83.1.

Techniques: Comparison, Control

Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet: Artesunate-Induced DNA Damage in P. falciparum Lab Strains (A) Schematic illustration of artesunate treatment based on Streptolysin O (SLO) enrichment (ring stage) or Percoll gradient centrifugation (schizont stage). (B) Artesunate-induced DNA damage in P. falciparum 3D7, Dd2, and Dd2 I543T . Ring-stage (upper panel) and schizont-stage (lower panel) P. falciparum parasites were treated with different concentrations of artesunate for 1 h and subjected to analysis on alkaline CometChip. On average, ~302 comets were analyzed per macrowell. Each experiment was done in technical triplicates, and data here were collected and are shown in biological triplicates or quadruplicates. ∗∗ p < 0.01; ∗∗∗ p < 0.001; ∗∗∗∗ p < 0.0001, one-way ANOVA. Dunnett’s multiple comparison tests were performed between vehicle control (0 μM) and respective concentrations. All data are indicated as means ± SEM.

Article Snippet: CometChip raw data and analyzed results, Part six , This paper; Mendeley data , https://doi.org/10.17632/grdkg7rb83.1.

Techniques: Gradient Centrifugation, Comparison, Control

Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet:

Article Snippet: CometChip raw data and analyzed results, Part six , This paper; Mendeley data , https://doi.org/10.17632/grdkg7rb83.1.

Techniques: Recombinant, Giemsa Stain, Saline, Purification, Plasmid Preparation, Software

Journal: Frontiers in Public Health

Article Title: A Modern Genotoxicity Testing Paradigm: Integration of the High-Throughput CometChip® and the TGx-DDI Transcriptomic Biomarker in Human HepaRG™ Cell Cultures

doi: 10.3389/fpubh.2021.694834

Figure Lengend Snippet: DNA damage in human HepaRG™ cells measured using the alkaline CometChip ® assay. Cells were exposed to increasing concentrations of DNA damage-inducing (DDI; A–I) and non-DDI test chemicals (J–L) . Median % tail DNA is shown 4 h following the last exposure. The data are expressed as the median % tail DNA ± SE ( n = 4). Red bars represent Group 1 DDI chemicals, blue bars denote the Group 2 non-DDI chemical and the Group 3 potentially misleading positive chemicals. Diagonal lines indicate overtly cytotoxic concentrations. Note the difference in the scale of the y-axis for MMS, ENU, and ZDV due to the large magnitude of the response for these three DDI (Group 1) chemicals. * P < 0.05, ** P < 0.001 compared to matched vehicle control.

Article Snippet: The chemical exposures in HepaRGTM cells, the cell viability studies, and the paired high-throughput CometChip ® analysis were conducted at Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, Durham, NC, USA).

Techniques: Control

Journal: Frontiers in Public Health

Article Title: A Modern Genotoxicity Testing Paradigm: Integration of the High-Throughput CometChip® and the TGx-DDI Transcriptomic Biomarker in Human HepaRG™ Cell Cultures

doi: 10.3389/fpubh.2021.694834

Figure Lengend Snippet: Summary of CometChip ® analysis and TempO-Seq ® TGx-DDI classification results for 12 test chemicals.

Article Snippet: The chemical exposures in HepaRGTM cells, the cell viability studies, and the paired high-throughput CometChip ® analysis were conducted at Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, Durham, NC, USA).

Techniques: Gene Expression

Journal: Frontiers in Public Health

Article Title: A Modern Genotoxicity Testing Paradigm: Integration of the High-Throughput CometChip® and the TGx-DDI Transcriptomic Biomarker in Human HepaRG™ Cell Cultures

doi: 10.3389/fpubh.2021.694834

Figure Lengend Snippet: Comparison of benchmark concentrations for CometChip ® (BMC CC ) and TGx-DDI biomarker genes (BMC TGx ).

Article Snippet: The chemical exposures in HepaRGTM cells, the cell viability studies, and the paired high-throughput CometChip ® analysis were conducted at Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, Durham, NC, USA).

Techniques: Comparison, Biomarker Discovery

Journal: Frontiers in Public Health

Article Title: A Modern Genotoxicity Testing Paradigm: Integration of the High-Throughput CometChip® and the TGx-DDI Transcriptomic Biomarker in Human HepaRG™ Cell Cultures

doi: 10.3389/fpubh.2021.694834

Figure Lengend Snippet: Relationship between the BMCs of the CometChip ® data (BMC CC ) and the TGx-DDI biomarker genes (BMC TGx ) for the test chemicals that yielded positive hazard calls in both tests and could be modeled. Specifically, the BMC CC with a BMR of 1SD with two-sided 95% CIs are shown for the CometChip ® vs. median bootstrap BMC TGX (BMR of 1SD) with two-sided 95% CIs for the TGx-DDI biomarker classification endpoint. The BMCs for the agents that were classified as DDI from both approaches were within 10-fold. The two parallel black lines with intercepts of 1 and −1 on the double log10 scale represent a 10-fold deviation from the 1:1 line.

Article Snippet: The chemical exposures in HepaRGTM cells, the cell viability studies, and the paired high-throughput CometChip ® analysis were conducted at Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, Durham, NC, USA).

Techniques: Biomarker Discovery

Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet: Optimization of CometChip (A and B) Representative pictures of “comet” of ring and schizont-stage P. falciparum 3D7 after on-chip hydrogen peroxide (H 2 O 2 ) treatment. Each green dot indicates a microwell in the CometChip. Each macrowell of the 96-well plate contains around ~300 of such microwells. The magnified view of the boxed area below shows the differentiation of head (between the green line and red line) and tail (between the red line and blue line) of an individual comet. This process would be automatically done by the algorithm as shown in the . Scale bars, 50 nm. (C) Quantification of “comet” after treatment. The y axis represents the percentage of DNA at the “comet” tail (%Tail DNA). On average, ~306 comets were analyzed per macrowell. Each experiment was done in technical triplicates, and data here were collected and are shown in biological triplicates. ∗ p < 0.05; ∗∗ p < 0.01, one-way analysis of variance (ANOVA). Dunnett’s multiple comparison tests were performed between vehicle control (0 μM) and respective concentrations. All data are indicated as means ± SEM.

Article Snippet: CometChip raw data and analyzed results, Part one , This paper; Mendeley data , https://doi.org/10.17632/dfgj5ymxn7.1.

Techniques: Comparison, Control

Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet: Artesunate-Induced DNA Damage in P. falciparum Lab Strains (A) Schematic illustration of artesunate treatment based on Streptolysin O (SLO) enrichment (ring stage) or Percoll gradient centrifugation (schizont stage). (B) Artesunate-induced DNA damage in P. falciparum 3D7, Dd2, and Dd2 I543T . Ring-stage (upper panel) and schizont-stage (lower panel) P. falciparum parasites were treated with different concentrations of artesunate for 1 h and subjected to analysis on alkaline CometChip. On average, ~302 comets were analyzed per macrowell. Each experiment was done in technical triplicates, and data here were collected and are shown in biological triplicates or quadruplicates. ∗∗ p < 0.01; ∗∗∗ p < 0.001; ∗∗∗∗ p < 0.0001, one-way ANOVA. Dunnett’s multiple comparison tests were performed between vehicle control (0 μM) and respective concentrations. All data are indicated as means ± SEM.

Article Snippet: CometChip raw data and analyzed results, Part one , This paper; Mendeley data , https://doi.org/10.17632/dfgj5ymxn7.1.

Techniques: Gradient Centrifugation, Comparison, Control

Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet:

Article Snippet: CometChip raw data and analyzed results, Part one , This paper; Mendeley data , https://doi.org/10.17632/dfgj5ymxn7.1.

Techniques: Recombinant, Giemsa Stain, Saline, Purification, Plasmid Preparation, Software

Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet: Optimization of CometChip (A and B) Representative pictures of “comet” of ring and schizont-stage P. falciparum 3D7 after on-chip hydrogen peroxide (H 2 O 2 ) treatment. Each green dot indicates a microwell in the CometChip. Each macrowell of the 96-well plate contains around ~300 of such microwells. The magnified view of the boxed area below shows the differentiation of head (between the green line and red line) and tail (between the red line and blue line) of an individual comet. This process would be automatically done by the algorithm as shown in the . Scale bars, 50 nm. (C) Quantification of “comet” after treatment. The y axis represents the percentage of DNA at the “comet” tail (%Tail DNA). On average, ~306 comets were analyzed per macrowell. Each experiment was done in technical triplicates, and data here were collected and are shown in biological triplicates. ∗ p < 0.05; ∗∗ p < 0.01, one-way analysis of variance (ANOVA). Dunnett’s multiple comparison tests were performed between vehicle control (0 μM) and respective concentrations. All data are indicated as means ± SEM.

Article Snippet: CometChip raw data and analyzed results, Part five , This paper; Mendeley data , https://doi.org/10.17632/8gsnzy5ndj.1.

Techniques: Comparison, Control

Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet: Artesunate-Induced DNA Damage in P. falciparum Lab Strains (A) Schematic illustration of artesunate treatment based on Streptolysin O (SLO) enrichment (ring stage) or Percoll gradient centrifugation (schizont stage). (B) Artesunate-induced DNA damage in P. falciparum 3D7, Dd2, and Dd2 I543T . Ring-stage (upper panel) and schizont-stage (lower panel) P. falciparum parasites were treated with different concentrations of artesunate for 1 h and subjected to analysis on alkaline CometChip. On average, ~302 comets were analyzed per macrowell. Each experiment was done in technical triplicates, and data here were collected and are shown in biological triplicates or quadruplicates. ∗∗ p < 0.01; ∗∗∗ p < 0.001; ∗∗∗∗ p < 0.0001, one-way ANOVA. Dunnett’s multiple comparison tests were performed between vehicle control (0 μM) and respective concentrations. All data are indicated as means ± SEM.

Article Snippet: CometChip raw data and analyzed results, Part five , This paper; Mendeley data , https://doi.org/10.17632/8gsnzy5ndj.1.

Techniques: Gradient Centrifugation, Comparison, Control

Journal: Cell Reports

Article Title: K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair

doi: 10.1016/j.celrep.2020.107996

Figure Lengend Snippet:

Article Snippet: CometChip raw data and analyzed results, Part five , This paper; Mendeley data , https://doi.org/10.17632/8gsnzy5ndj.1.

Techniques: Recombinant, Giemsa Stain, Saline, Purification, Plasmid Preparation, Software