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Processes 2014, 2(1), 218-237; doi:10.3390/pr2010218
Article

Interpretation of Cellular Imaging and AQP4 Quantification Data in a Single Cell Simulator

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Received: 22 July 2013; in revised form: 21 January 2014 / Accepted: 22 January 2014 / Published: 4 March 2014
(This article belongs to the Special Issue Feature Papers)
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Abstract: The goal of the present study is to integrate different datasets in cell biology to derive additional quantitative information about a gene or protein of interest within a single cell using computational simulations. We propose a novel prototype cell simulator as a quantitative tool to integrate datasets including dynamic information about transcript and protein levels and the spatial information on protein trafficking in a complex cellular geometry. In order to represent the stochastic nature of transcription and gene expression, our cell simulator uses event-based stochastic simulations to capture transcription, translation, and dynamic trafficking events. In a reconstructed cellular geometry, a realistic microtubule structure is generated with a novel growth algorithm for simulating vesicular transport and trafficking events. In a case study, we investigate the change in quantitative expression levels of a water channel-aquaporin 4-in a single astrocyte cell, upon pharmacological treatment. Gillespie based discrete time approximation method results in stochastic fluctuation of mRNA and protein levels. In addition, we compute the dynamic trafficking of aquaporin-4 on microtubules in this reconstructed astrocyte. Computational predictions are validated with experimental data. The demonstrated cell simulator facilitates the analysis and prediction of protein expression dynamics.
Keywords: stochastic simulation; aquaporin 4; cell molecular simulator; systems biology stochastic simulation; aquaporin 4; cell molecular simulator; systems biology
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Kim, S.B.; Hsu, Y.; Linninger, A.A. Interpretation of Cellular Imaging and AQP4 Quantification Data in a Single Cell Simulator. Processes 2014, 2, 218-237.

AMA Style

Kim SB, Hsu Y, Linninger AA. Interpretation of Cellular Imaging and AQP4 Quantification Data in a Single Cell Simulator. Processes. 2014; 2(1):218-237.

Chicago/Turabian Style

Kim, Seon B.; Hsu, Ying; Linninger, Andreas A. 2014. "Interpretation of Cellular Imaging and AQP4 Quantification Data in a Single Cell Simulator." Processes 2, no. 1: 218-237.

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