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Time-resolved cell culture assay analyser (TReCCA Analyser) for the analysis of on-line data: data integration--sensor correction--time-resolved IC50 determination.

Lochead J, Schessner J, Werner T, Wölfl S - PLoS ONE (2015)

Bottom Line: The functions of the program include data normalising and averaging, as well as smoothing and slope calculation, pin-pointing exact change time points.To illustrate the capabilities of the TReCCA Analyser, we performed on-line monitoring of dissolved oxygen in the culture media of the breast cancer cell line MCF-7 treated with different concentrations of the anti-cancer drug Cisplatin.The TReCCA Analyser is freely available at www.uni-heidelberg.de/fakultaeten/biowissenschaften/ipmb/biologie/woelfl/Research.html.

View Article: PubMed Central - PubMed

Affiliation: Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany; Institute for Analytical Chemistry, Mannheim University of Applied Sciences, Mannheim, Germany.

ABSTRACT
Time-resolved cell culture assays circumvent the need to set arbitrary end-points and reveal the dynamics of quality controlled experiments. However, they lead to the generation of large data sets, which can represent a complexity barrier to their use. We therefore developed the Time-Resolved Cell Culture Assay (TReCCA) Analyser program to perform standard cell assay analyses efficiently and make sophisticated in-depth analyses easily available. The functions of the program include data normalising and averaging, as well as smoothing and slope calculation, pin-pointing exact change time points. A time-resolved IC50/EC50 calculation provides a better understanding of drug toxicity over time and a more accurate drug to drug comparison. Finally the logarithmic sensor recalibration function, for sensors with an exponential calibration curve, homogenises the sensor output and enables the detection of low-scale changes. To illustrate the capabilities of the TReCCA Analyser, we performed on-line monitoring of dissolved oxygen in the culture media of the breast cancer cell line MCF-7 treated with different concentrations of the anti-cancer drug Cisplatin. The TReCCA Analyser is freely available at www.uni-heidelberg.de/fakultaeten/biowissenschaften/ipmb/biologie/woelfl/Research.html. By introducing the program, we hope to encourage more systematic use of time-resolved assays and lead researchers to fully exploit their data.

No MeSH data available.


Related in: MedlinePlus

Medium oxygen level of MCF-7 cells when exposed to different concentrations of Cisplatin over time.All the sensors are measured empty for sensor calibration between minutes 0 and 136 (A), then a sensor calibration is performed (B), followed by normalisation to the wells containing only medium (C). The whole time frame of the experiment is visible in the raw data (D): MCF-7 cell seeding at 136 min, medium change at day 1.09 and Cisplatin addition at different concentrations at day 2.1. The sensor correction and the normalisation to the conditions containing only medium are applied to all the data (E, F respectively). The time points used for sensor correction/normalisation (A, B, C) are depicted as black rectangles (D, E, F respectively). The triplicates of the sensor corrected and normalised data are averaged (G) and their standard deviation is displayed as a grey shadow around each curve. The legend at the bottom of the figure is valid for all the subfigures, microM stands for micromolar. These graphs are displayed as they are produced by the TReCCA Analyser.
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pone.0131233.g002: Medium oxygen level of MCF-7 cells when exposed to different concentrations of Cisplatin over time.All the sensors are measured empty for sensor calibration between minutes 0 and 136 (A), then a sensor calibration is performed (B), followed by normalisation to the wells containing only medium (C). The whole time frame of the experiment is visible in the raw data (D): MCF-7 cell seeding at 136 min, medium change at day 1.09 and Cisplatin addition at different concentrations at day 2.1. The sensor correction and the normalisation to the conditions containing only medium are applied to all the data (E, F respectively). The time points used for sensor correction/normalisation (A, B, C) are depicted as black rectangles (D, E, F respectively). The triplicates of the sensor corrected and normalised data are averaged (G) and their standard deviation is displayed as a grey shadow around each curve. The legend at the bottom of the figure is valid for all the subfigures, microM stands for micromolar. These graphs are displayed as they are produced by the TReCCA Analyser.

Mentions: The MCF-7 and Cisplatin treatment data was extracted from the software provided with the SDR reader (SDR version v38), which is required for recording but does not enable adequate analysis of the data obtained. The TReCCA Analyser provides analysis options and plotting possibilities for the SDR data, but is also suitable for any other type of large time-resolved analytical measurements. The time scale was first converted from seconds to days. The last part of the graph is excluded, as after day 5 the viability of the controls decreases due to the lack of medium change. The raw data obtained after basic data formatting can be seen in Fig 2D. The cells seeded on the first day reduce the level of dissolved oxygen, which is replenished after medium change in the second day. The dissolved oxygen is then reduced again but this time in a more homogeneous way and to a lesser extent as the cell adhesion process does not interfere with the basal cell respiration levels. Starting on the third day, the dissolved oxygen level depends on the Cisplatin concentration: high Cisplatin concentrations lead to cell death and higher dissolved oxygen values. The cells in the non-treated condition reach confluence, the cell number and thereby the total oxygen consumption becomes constant as reflected by the stable dissolved oxygen values.


Time-resolved cell culture assay analyser (TReCCA Analyser) for the analysis of on-line data: data integration--sensor correction--time-resolved IC50 determination.

Lochead J, Schessner J, Werner T, Wölfl S - PLoS ONE (2015)

Medium oxygen level of MCF-7 cells when exposed to different concentrations of Cisplatin over time.All the sensors are measured empty for sensor calibration between minutes 0 and 136 (A), then a sensor calibration is performed (B), followed by normalisation to the wells containing only medium (C). The whole time frame of the experiment is visible in the raw data (D): MCF-7 cell seeding at 136 min, medium change at day 1.09 and Cisplatin addition at different concentrations at day 2.1. The sensor correction and the normalisation to the conditions containing only medium are applied to all the data (E, F respectively). The time points used for sensor correction/normalisation (A, B, C) are depicted as black rectangles (D, E, F respectively). The triplicates of the sensor corrected and normalised data are averaged (G) and their standard deviation is displayed as a grey shadow around each curve. The legend at the bottom of the figure is valid for all the subfigures, microM stands for micromolar. These graphs are displayed as they are produced by the TReCCA Analyser.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482264&req=5

pone.0131233.g002: Medium oxygen level of MCF-7 cells when exposed to different concentrations of Cisplatin over time.All the sensors are measured empty for sensor calibration between minutes 0 and 136 (A), then a sensor calibration is performed (B), followed by normalisation to the wells containing only medium (C). The whole time frame of the experiment is visible in the raw data (D): MCF-7 cell seeding at 136 min, medium change at day 1.09 and Cisplatin addition at different concentrations at day 2.1. The sensor correction and the normalisation to the conditions containing only medium are applied to all the data (E, F respectively). The time points used for sensor correction/normalisation (A, B, C) are depicted as black rectangles (D, E, F respectively). The triplicates of the sensor corrected and normalised data are averaged (G) and their standard deviation is displayed as a grey shadow around each curve. The legend at the bottom of the figure is valid for all the subfigures, microM stands for micromolar. These graphs are displayed as they are produced by the TReCCA Analyser.
Mentions: The MCF-7 and Cisplatin treatment data was extracted from the software provided with the SDR reader (SDR version v38), which is required for recording but does not enable adequate analysis of the data obtained. The TReCCA Analyser provides analysis options and plotting possibilities for the SDR data, but is also suitable for any other type of large time-resolved analytical measurements. The time scale was first converted from seconds to days. The last part of the graph is excluded, as after day 5 the viability of the controls decreases due to the lack of medium change. The raw data obtained after basic data formatting can be seen in Fig 2D. The cells seeded on the first day reduce the level of dissolved oxygen, which is replenished after medium change in the second day. The dissolved oxygen is then reduced again but this time in a more homogeneous way and to a lesser extent as the cell adhesion process does not interfere with the basal cell respiration levels. Starting on the third day, the dissolved oxygen level depends on the Cisplatin concentration: high Cisplatin concentrations lead to cell death and higher dissolved oxygen values. The cells in the non-treated condition reach confluence, the cell number and thereby the total oxygen consumption becomes constant as reflected by the stable dissolved oxygen values.

Bottom Line: The functions of the program include data normalising and averaging, as well as smoothing and slope calculation, pin-pointing exact change time points.To illustrate the capabilities of the TReCCA Analyser, we performed on-line monitoring of dissolved oxygen in the culture media of the breast cancer cell line MCF-7 treated with different concentrations of the anti-cancer drug Cisplatin.The TReCCA Analyser is freely available at www.uni-heidelberg.de/fakultaeten/biowissenschaften/ipmb/biologie/woelfl/Research.html.

View Article: PubMed Central - PubMed

Affiliation: Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany; Institute for Analytical Chemistry, Mannheim University of Applied Sciences, Mannheim, Germany.

ABSTRACT
Time-resolved cell culture assays circumvent the need to set arbitrary end-points and reveal the dynamics of quality controlled experiments. However, they lead to the generation of large data sets, which can represent a complexity barrier to their use. We therefore developed the Time-Resolved Cell Culture Assay (TReCCA) Analyser program to perform standard cell assay analyses efficiently and make sophisticated in-depth analyses easily available. The functions of the program include data normalising and averaging, as well as smoothing and slope calculation, pin-pointing exact change time points. A time-resolved IC50/EC50 calculation provides a better understanding of drug toxicity over time and a more accurate drug to drug comparison. Finally the logarithmic sensor recalibration function, for sensors with an exponential calibration curve, homogenises the sensor output and enables the detection of low-scale changes. To illustrate the capabilities of the TReCCA Analyser, we performed on-line monitoring of dissolved oxygen in the culture media of the breast cancer cell line MCF-7 treated with different concentrations of the anti-cancer drug Cisplatin. The TReCCA Analyser is freely available at www.uni-heidelberg.de/fakultaeten/biowissenschaften/ipmb/biologie/woelfl/Research.html. By introducing the program, we hope to encourage more systematic use of time-resolved assays and lead researchers to fully exploit their data.

No MeSH data available.


Related in: MedlinePlus