Are Assumptions about the Model Type Necessary in Reaction-Diffusion Modeling? A FRAP Application

Mai, Juliane; Trump, Saskia; Ali, Rizwan; Schiltz, R. Louis; Hager, Gordon L.; Hanke, Thomas; Lehmann, Irina; Attinger, Sabine

doi:10.1016/j.bpj.2011.01.041

Cited by 20 publications

(22 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The time constant (τ) of recovery or spread correlates with junctional permeability 9 . Limitations include the interpretation of time constants, which is neither standardized nor absolute; the extraction of τ, which depends on the mathematical model used 13,14 ; the use of dyes of different molecular weight and diffusion rate, which can lead to different time constants for the same model 15 and the results of which need to be calibrated. The benefit of these methods is their applicability to a multicellular setting, unlike the dual-cell patch clamp.…”

Section: Existing Methods For Assessment Of Intercellular Couplingmentioning

confidence: 99%

OptoGap: an optogenetics-enabled assay for quantification of cell-cell coupling in multicellular cardiac tissue

Jia

Boyle

Klimas

et al. 2017

Preprint

View full text Add to dashboard Cite

Intercellular electrical coupling is an essential means of communication between cells. It is important to obtain quantitative knowledge of such coupling between cardiomyocytes and nonexcitable cells when, for example, pathological electrical coupling between myofibroblasts and cardiomyocytes yields increased arrhythmia risk or during the integration of donor (e.g. cardiac progenitor) cells with native cardiomyocytes in cell-therapy approaches. Currently, there is no direct method for assessing heterocellular coupling within multicellular tissue. Here we demonstrate experimentally and computationally a new contactless assay for electrical coupling, OptoGap, based on selective illumination of inexcitable cells that express optogenetic actuators and optical sensing of the response of coupled excitable cells, e.g. cardiomyocytes, that are lightinsensitive. Cell-cell coupling is quantified by the energy required to elicit an action potential via junctional current from the light-stimulated cell(s). The proposed technique is experimentally validated against the standard indirect approach, GapFRAP, using light-sensitive cardiac fibroblasts and non-transformed cardiomyocytes in a two-dimensional setting. It's potential applicability to the complex three-dimensional setting of the native heart is corroborated by computational modeling and proper calibration.peer-reviewed)

show abstract

Section: Existing Methods For Assessment Of Intercellular Couplingmentioning

confidence: 99%

OptoGap: an optogenetics-enabled assay for quantification of cell-cell coupling in multicellular cardiac tissue

Jia

Boyle

Klimas

et al. 2017

Preprint

View full text Add to dashboard Cite

show abstract

“…Murine hepatoma cells (Hepa1c1c7, LGC Standards GmbH, Wesel, Germany) and GFP-AhR expressing cells ("Tet-Off System" previously described in [29]) were cultured in Dulbecco's Modified Eagle's Medium (Biochrom AG, Berlin, Germany) supplemented with 10% fetal bovine serum (FBS, Biochrom), 1% L-alanyl-L-glutamine (Biochrom), and 1% penicillin/ streptomycin (Biochrom). To prevent GFP-AhR expression, medium was supplemented with 5 mg/ml tetracycline (Tet).…”

Section: Cell Culture Of Hepa1c1c7 Cell Linementioning

confidence: 99%

Live cell imaging of the intracellular compartmentalization of the contaminate benzo[a]pyrene

Ali

Trump

Lehmann

et al. 2014

Journal of Biophotonics

Self Cite

View full text Add to dashboard Cite

This study investigates the cellular response of murine hepatoma cells to the polycyclic aromatic hydrocarbon benzo[a]pyrene (B[a]P) using two-photon and confocal laser scanning microscopy. The intracellular distribution of B[a]P and the B[a]P/AhR complex was visualized time- and concentration-dependent for up to 48 h of exposure. B[a]P was predominantly found in lipid droplets, endoplasmic reticulum and lysosomes, where B[a]P is collected and forms large aggregates. Changes in mitochondrial membrane potential and bleb formation due to high B[a]P concentrations were observed. The imaging data presented in this study provide new insights into the systemic cellular regulation following B[a]P exposure.

show abstract

“…The parameter estimation step consists in fitting this data with a ‘suitable’ model, but since the recovery portion typically can be fit with a sum of time-dependent exponential terms (Mai et al 2011), this leaves wide latitude as to what underlying processes are to be included, and once that is fixed, what meaning can be ascribed to those parameters. Traditionally FRAP experiments were used for cellular or sub-cellular level processes that occur on short time scales, and by fitting parameters such as diffusion coefficients and binding rates to the data, properties of cell- or sub-cellular-level processes could be inferred.…”

Section: Introductionmentioning

confidence: 99%

Improving Parameter Inference from FRAP Data: an Analysis Motivated by Pattern Formation in the Drosophila Wing Disc

Lin

Othmer

2017

Bull Math Biol

View full text Add to dashboard Cite

Fluorescence recovery after photobleaching (FRAP) is used to obtain quantitative information about molecular diffusion and binding kinetics at both cell and tissue levels of organization. FRAP models have been proposed to estimate the diffusion coefficients and binding kinetic parameters of species for a variety of biological systems and experimental settings. However it is not clear what the connection among the diverse parameter estimates from different models of the same system is, whether the assumptions made in the model are appropriate, and what the qualities of the estimates are. Here we propose a new approach to investigate the discrepancies between parameters estimated from different models. We use a theoretical model to simulate the dynamics of a FRAP experiment and generate the data that is used in various recovery models to estimate the corresponding parameters. By postulating a recovery model identical to the theoretical model, we first establish that the appropriate choice of observation time can significantly improve the quality of estimates, especially when the diffusion and binding kinetics are not well balanced, in a sense made precise later. Secondly, we find that changing the balance between diffusion and binding kinetics by changing the size of the bleaching region, which gives rise to different FRAP curves, provides a priori knowledge of diffusion and binding kinetics, which is important for model formulation. We also show that the use of the spatial information in FRAP provides better parameter estimation. By varying the recovery model from a fixed theoretical model, we show that a simplified recovery model can adequately describe the FRAP process in some circumstances, and establish the relationship between parameters in the theoretical model and those in the recovery model. We then analyze an example in which the data is generated with a model of intermediate complexity and the parameters are estimated using models of greater or less complexity, and show how sensitivity analysis can be used to improve FRAP model formulation. Lastly, we show how sophisticated global sensitivity analysis can be used to detect over-fitting with a model being too complex.

show abstract

Are Assumptions about the Model Type Necessary in Reaction-Diffusion Modeling? A FRAP Application

Cited by 20 publications

References 45 publications

OptoGap: an optogenetics-enabled assay for quantification of cell-cell coupling in multicellular cardiac tissue

OptoGap: an optogenetics-enabled assay for quantification of cell-cell coupling in multicellular cardiac tissue

Live cell imaging of the intracellular compartmentalization of the contaminate benzo[a]pyrene

Improving Parameter Inference from FRAP Data: an Analysis Motivated by Pattern Formation in the Drosophila Wing Disc

Contact Info

Product

Resources

About