Single-Particle Tracking Reveals Anti-Persistent Subdiffusion in Cell Extracts

Abstract

Single-particle tracking (SPT) has become a powerful tool to quantify transport phenomena in complex media with unprecedented detail. Based on the reconstruction of individual trajectories, a wealth of informative measures become available for each particle, allowing for a detailed comparison with theoretical predictions. While SPT has been used frequently to explore diffusive transport in artificial fluids and inside living cells, intermediate systems, i.e., biochemically active cell extracts, have been studied only sparsely. Extracts derived from the eggs of the clawfrog Xenopus laevis, for example, are known for their ability to support and mimic vital processes of cells, emphasizing the need to explore also the transport phenomena of nano-sized particles in such extracts. Here, we have performed extensive SPT on beads with 20 nm radius in native and chemically treated Xenopus extracts. By analyzing a variety of distinct measures, we show that these beads feature an anti-persistent subdiffusion that is consistent with fractional Brownian motion. Chemical treatments did not grossly alter this finding, suggesting that the high degree of macromolecular crowding in Xenopus extracts equips the fluid with a viscoelastic modulus, hence enforcing particles to perform random walks with a significant anti-persistent memory kernel.

Extracting, quantifying, and comparing dynamical and biomechanical properties of living matter through single particle tracking

“…Detailed analyses for Brownian and fractional Brownian motion demonstrate that the power-law decay S k ( f , T ) ∼ 1/ f β is preserved in individual PSDs. In addition, similarly to the amplitude variations of the TA-MSD from one finite-time trajectory to the next, the PDF P k ( A ) of fluctuations of the PSD's amplitude A for different trajectories from the same ensemble show a characteristic behaviour, which has also been verified with experimental data, 154,210–212 as shown in the inset of Fig. 5c.…”

Anomalous diffusion, aging, and nonergodicity of scaled Brownian motion with fractional Gaussian noise: overview of related experimental observations and models

“…The model of antipersistent subdiffusive FBM-including the situations with ensemble-distributed values of 2H and K 2H -has been successfully applied to the description of the spreading characteristics of tracers of various nature in living biological cells 13,140,[156][157][158][159] as well as in various prototypical in vitro crowded environments 8,[160][161][162][163] (sucrose, dextran, mucin, etc.) mimicking the macromolecularly crowded cyto-and nucleoplasm of a cell.…”

Probing local chromatin dynamics by tracking telomeres

“…The PDF of generalized diffusion coefficients, p(K), obtained from fitting in intervals (A) or (B) both feature a roughly lognormal shape (see [15] for a discussion of this fairly common observation) with comparable peak positions but slightly different widths (Fig. 2c).…”

“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted February 16, 2022. ; https://doi.org/10.1101/2022.02. 15.480529 doi: bioRxiv preprint partially driven by active noise mediated by the cytoskeleton. Going beyond these results, we show here that the subdiffusion of telomeres bears all features of a fractional Brownian motion (FBM) process with intermittent jumps between apparent niches, supposedly formed by the surrounding chromatin.…”