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Quantification of nuclear transport in single cells

Lucía Durrieu, Rikard Johansson, Alan Bush, David Janzén, Martin Gollvik, Gunnar Cedersund, Alejandro Colman-Lerner
doi: https://doi.org/10.1101/001768
Lucía Durrieu
1Institute of Physiology, Molecular Biology and Neurosciences, National Research Council and Department of Physiology, Molecular and Cell Biology, School of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
2Present addresses: EMBL Heidelberg, Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, Deutsches Krebsforschungszentrum, DKFZ–ZMBH Allianz, Heidelberg, Germany
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Rikard Johansson
3Department of Biomedical Engineering, Linköping University, Linköping, Sweden
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Alan Bush
1Institute of Physiology, Molecular Biology and Neurosciences, National Research Council and Department of Physiology, Molecular and Cell Biology, School of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
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David Janzén
3Department of Biomedical Engineering, Linköping University, Linköping, Sweden
4Present addresses: Biomedical and Biological Systems Laboratory, School of Engineering, University of Warwick, Coventry, UK; AstraZeneca, Mölndal, Sweden; Department of Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, Sweden
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Martin Gollvik
3Department of Biomedical Engineering, Linköping University, Linköping, Sweden
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Gunnar Cedersund
3Department of Biomedical Engineering, Linköping University, Linköping, Sweden
5Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
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Alejandro Colman-Lerner
1Institute of Physiology, Molecular Biology and Neurosciences, National Research Council and Department of Physiology, Molecular and Cell Biology, School of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
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Abstract

Regulation of nuclear transport is a key cellular function involved in many central processes, such as gene expression regulation and signal transduction. Rates of protein movement between cellular compartments can be measured by FRAP. However, no standard and reliable methods to calculate transport rates exist. Here we introduce a method to extract import and export rates, suitable for noisy single cell data. This method consists of microscope procedures, routines for data processing, an ODE model to fit to the data, and algorithms for parameter optimization and error estimation.

Using this method, we successfully measured import and export rates in individual yeast. For YFP, average transport rates were 0.15 sec-1. We estimated confidence intervals for these parameters through likelihood profile analysis. We found large cell-to-cell variation (CV = 0.79) in these rates, suggesting a hitherto unknown source of cellular heterogeneity. Given the passive nature of YFP diffusion, we attribute this variation to large differences among cells in the number or quality of nuclear pores.

Owing to its broad applicability and sensitivity, this method will allow deeper mechanistic insight into nuclear transport processes and into the largely unstudied cell-to-cell variation in kinetic rates.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND Unported 3.0 license.
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Posted January 13, 2014.
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Quantification of nuclear transport in single cells
Lucía Durrieu, Rikard Johansson, Alan Bush, David Janzén, Martin Gollvik, Gunnar Cedersund, Alejandro Colman-Lerner
bioRxiv 001768; doi: https://doi.org/10.1101/001768
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Quantification of nuclear transport in single cells
Lucía Durrieu, Rikard Johansson, Alan Bush, David Janzén, Martin Gollvik, Gunnar Cedersund, Alejandro Colman-Lerner
bioRxiv 001768; doi: https://doi.org/10.1101/001768

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