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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

Smoothing and slope calculation.The oxygen levels in the media of MCF-7 cells exposed to different Cisplatin concentrations (as depicted in Fig 2G) between day 2.2 and 5 (A) are smoothed (C) by replacing each time point by the average of an 11 time point-neighbourhood. The smoothing can be seen more precisely on a bigger scale as it is the case for 75–80% a.s. and day 3–3.5 by comparing the raw data (B) to the smoothed data (D). The slope of each time point (E) is then obtained by performing a linear fit of each point and 15 points on either side of it. The residual error of the fit is displayed as a grey shadow around each curve (very small in this case). The legend in Fig 3E is valid for all the subfigures, microM stands for micromolar.
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pone.0131233.g003: Smoothing and slope calculation.The oxygen levels in the media of MCF-7 cells exposed to different Cisplatin concentrations (as depicted in Fig 2G) between day 2.2 and 5 (A) are smoothed (C) by replacing each time point by the average of an 11 time point-neighbourhood. The smoothing can be seen more precisely on a bigger scale as it is the case for 75–80% a.s. and day 3–3.5 by comparing the raw data (B) to the smoothed data (D). The slope of each time point (E) is then obtained by performing a linear fit of each point and 15 points on either side of it. The residual error of the fit is displayed as a grey shadow around each curve (very small in this case). The legend in Fig 3E is valid for all the subfigures, microM stands for micromolar.

Mentions: For the next analysis steps, we focus on the data after Cisplatin treatment between day 2.2 and 5 (Fig 3A). The time frame could have been shifted to start at the time of treatment but was left for clarity. In order to determine the slope of the curves over time, the averaged data is first smoothened for n = 11 (Fig 3C) as can be seen more precisely at a bigger scale (Fig 3B and 3D). The slope of the smoothed data is then determined for n = 15 (Fig 3E). It reveals that the amount of dissolved oxygen increases first and fastest for the highest Cisplatin concentrations, its rate of change reaches a maximum and then decreases slowly until stabilising. Lower Cisplatin concentrations follow the same reaction pattern, however the initial speed of change in respiratory behaviour is slower. The non-treated condition and the lowest Cisplatin concentrations have a constant oxygen consumption during the course of the experiment, as the slope is close to zero. The slope calculation allows to pin-point the exact time when the change of respiration is highest or constant; it also leads to a more accurate comparison of the different Cisplatin concentrations.


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)

Smoothing and slope calculation.The oxygen levels in the media of MCF-7 cells exposed to different Cisplatin concentrations (as depicted in Fig 2G) between day 2.2 and 5 (A) are smoothed (C) by replacing each time point by the average of an 11 time point-neighbourhood. The smoothing can be seen more precisely on a bigger scale as it is the case for 75–80% a.s. and day 3–3.5 by comparing the raw data (B) to the smoothed data (D). The slope of each time point (E) is then obtained by performing a linear fit of each point and 15 points on either side of it. The residual error of the fit is displayed as a grey shadow around each curve (very small in this case). The legend in Fig 3E is valid for all the subfigures, microM stands for micromolar.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131233.g003: Smoothing and slope calculation.The oxygen levels in the media of MCF-7 cells exposed to different Cisplatin concentrations (as depicted in Fig 2G) between day 2.2 and 5 (A) are smoothed (C) by replacing each time point by the average of an 11 time point-neighbourhood. The smoothing can be seen more precisely on a bigger scale as it is the case for 75–80% a.s. and day 3–3.5 by comparing the raw data (B) to the smoothed data (D). The slope of each time point (E) is then obtained by performing a linear fit of each point and 15 points on either side of it. The residual error of the fit is displayed as a grey shadow around each curve (very small in this case). The legend in Fig 3E is valid for all the subfigures, microM stands for micromolar.
Mentions: For the next analysis steps, we focus on the data after Cisplatin treatment between day 2.2 and 5 (Fig 3A). The time frame could have been shifted to start at the time of treatment but was left for clarity. In order to determine the slope of the curves over time, the averaged data is first smoothened for n = 11 (Fig 3C) as can be seen more precisely at a bigger scale (Fig 3B and 3D). The slope of the smoothed data is then determined for n = 15 (Fig 3E). It reveals that the amount of dissolved oxygen increases first and fastest for the highest Cisplatin concentrations, its rate of change reaches a maximum and then decreases slowly until stabilising. Lower Cisplatin concentrations follow the same reaction pattern, however the initial speed of change in respiratory behaviour is slower. The non-treated condition and the lowest Cisplatin concentrations have a constant oxygen consumption during the course of the experiment, as the slope is close to zero. The slope calculation allows to pin-point the exact time when the change of respiration is highest or constant; it also leads to a more accurate comparison of the different Cisplatin concentrations.

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