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Mapping intracellular dynamics across the whole cell with spatial statistics.

Yohei Okabe1, Takumi Saito1, Outa Nakashima1

  • 1Graduate School of Engineering Science, The University of Osaka, Toyonaka, Osaka, Japan.

Biophysical Journal
|October 9, 2025
PubMed
Summary

We developed probabilistic FRAP (Pro-FRAP) to map whole-cell molecular diffusion. This method uses spatial statistics to estimate diffusion in unmeasured areas, improving understanding of intracellular transport.

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Area of Science:

  • Cellular biophysics
  • Molecular dynamics
  • Quantitative biology

Background:

  • Mapping intracellular molecular diffusion is vital for understanding cellular mechanisms.
  • Techniques like fluorescence recovery after photobleaching (FRAP) offer limited spatial data due to experimental constraints.
  • Deterministic interpolation methods fail to capture spatial variability in diffusion.

Purpose of the Study:

  • To develop a novel method for versatile whole-cell mapping of molecular diffusion.
  • To overcome the limitations of sparse data acquisition in live-cell measurements.
  • To provide a statistically robust estimation of diffusion in unmeasured cellular regions.

Main Methods:

  • Integration of fluorescence recovery after photobleaching (FRAP) with sequential Gaussian simulation (SGS).
  • Application of SGS for probabilistic modeling and estimation of diffusion in unmeasured regions.
  • Numerical simulations to optimize measurement point distribution for enhanced data accuracy.

Main Results:

  • Probabilistic FRAP (Pro-FRAP) enables statistically robust estimation of intracellular diffusion.
  • Pro-FRAP captures spatial variability and quantifies uncertainty, unlike deterministic methods.
  • Optimized measurement point arrangements improve data accuracy and coverage for diffusion mapping.

Conclusions:

  • Pro-FRAP offers a generalizable tool for whole-cell biophysical analysis under sparse sampling.
  • The approach enhances the detailed representation of molecular transport within cells.
  • Applicable to other intracellular dynamics like molecular turnover measurable at limited points.