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A Highly Accurate Pixel-Based FRAP Model Based on Spectral-Domain Numerical Methods
RISE - Research Institutes of Sweden, Biovetenskap och material, Jordbruk och livsmedel.ORCID-id: 0000-0002-5956-9934
RISE - Research Institutes of Sweden, Biovetenskap och material, Jordbruk och livsmedel.
RISE - Research Institutes of Sweden, Biovetenskap och material, Jordbruk och livsmedel.
Chalmers University of Technology, Sweden.
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2019 (engelsk)Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 116, nr 7, s. 1348-1361Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

We introduce a new, to our knowledge, numerical model based on spectral methods for analysis of fluorescence recovery after photobleaching data. The model covers pure diffusion and diffusion and binding (reaction-diffusion) with immobile binding sites, as well as arbitrary bleach region shapes. Fitting of the model is supported using both conventional recovery-curve-based estimation and pixel-based estimation, in which all individual pixels in the data are utilized. The model explicitly accounts for multiple bleach frames, diffusion (and binding) during bleaching, and bleaching during imaging. To our knowledge, no other fluorescence recovery after photobleaching framework incorporates all these model features and estimation methods. We thoroughly validate the model by comparison to stochastic simulations of particle dynamics and find it to be highly accurate. We perform simulation studies to compare recovery-curve-based estimation and pixel-based estimation in realistic settings and show that pixel-based estimation is the better method for parameter estimation as well as for distinguishing pure diffusion from diffusion and binding. We show that accounting for multiple bleach frames is important and that the effect of neglecting this is qualitatively different for the two estimation methods. We perform a simple experimental validation showing that pixel-based estimation provides better agreement with literature values than recovery-curve-based estimation and that accounting for multiple bleach frames improves the result. Further, the software developed in this work is freely available online.

sted, utgiver, år, opplag, sider
2019. Vol. 116, nr 7, s. 1348-1361
HSV kategori
Identifikatorer
URN: urn:nbn:se:ri:diva-38231DOI: 10.1016/j.bpj.2019.02.023Scopus ID: 2-s2.0-85062705820OAI: oai:DiVA.org:ri-38231DiVA, id: diva2:1299501
Merknad

 Funding details: Vetenskapsrådet, 2016-03809; Funding details: Stiftelsen för Strategisk Forskning; Funding text 1: The financial support of the VINN Excellence Centre SuMo Biomaterials , the Swedish Foundation for Strategic Research project “Material structures seen through microscopes and statistics,” and the Swedish Research Council (grant number 2016-03809 ) is acknowledged. The computations were in part performed on resources at Chalmers Centre for Computational Science and Engineering provided by the Swedish National Infrastructure for Computing.

Tilgjengelig fra: 2019-03-27 Laget: 2019-03-27 Sist oppdatert: 2019-06-28bibliografisk kontrollert

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