Time-heterogeneity of the Förster Radius from Dipole Orientational Dynamics Explains Observed Dynamic Shift.

Förster resonance energy transfer (FRET) is a quantum mechanical phenomenon involving the non-radiative transfer of energy between coupled electric dipoles. Due to the strong dependence of FRET on the distance between the dipoles, it is frequently used as a "molecular ruler" in biology, chemistry, and physics. This is done by placing dipolar molecules called dyes on molecules of interest. In time-resolved confocal single-molecule FRET (smFRET) experiments, the joint distribution of the FRET efficiency and the donor fluorescence lifetime can reveal underlying molecular conformational dynamics via deviation from their theoretical Förster relationship. This deviation is referred to as a dynamic shift. Quantifying the dynamic shift caused by the motion of the fluorescent dyes is essential to decoupling the dynamics of the studied molecules and the dyes. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based on first physics principles and proper dye linker chemistry to match accessible volumes predicted by molecular dynamics simulations. By simulating the dyes' stochastic translational and rotational dynamics, we show that the observed dynamic shift can largely be attributed to the mutual orientational dynamics of the electric dipole moments associated with the dyes, not their accessible volume.

Palmitate-mediated disruption of the endoplasmic reticulum decreases intracellular vesicle motility.

Essential cellular processes such as metabolism, protein synthesis, and autophagy require the intracellular transport of membrane-bound vesicles. The importance of the cytoskeleton and associated molecular motors for transport is well documented. Recent research has suggested that the endoplasmic reticulum (ER) may also play a role in vesicle transport through a tethering of vesicles to the ER. We use single-particle tracking fluorescence microscopy and a Bayesian change-point algorithm to characterize vesicle motility in response to the disruption of the ER, actin, and microtubules. This high-throughput change-point algorithm allows us to efficiently analyze thousands of trajectory segments. We find that palmitate-mediated disruption of the ER leads to a significant decrease in vesicle motility. A comparison with the disruption of actin and microtubules shows that disruption of the ER has a significant impact on vesicle motility, greater than the disruption of actin. Vesicle motility was dependent on cellular region, with greater motility in the cell periphery than the perinuclear region, possibly due to regional differences in actin and the ER. Overall, these results suggest that the ER is an important factor in vesicle transport.

Transport of lysosomes decreases in the perinuclear region: Insights from changepoint analysis.

Lysosomes are membrane-bound organelles that serve as the endpoint for endocytosis, phagocytosis, and autophagy, degrading the molecules, pathogens, and organelles localized within them. These cellular functions require intracellular transport. We use fluorescence microscopy to characterize the motion of lysosomes as a function of intracellular region, perinuclear or periphery, and lysosome diameter. Single-particle tracking data are complemented by changepoint identification and analysis of a mathematical model for state switching. We first classify lysosomal motion as motile or stationary. We then study how lysosome location and diameter affects the proportion of time spent in each state and quantify the speed during motile periods. We find that the proportion of time spent stationary is strongly region dependent, with significantly decreased motility in the perinuclear region. Increased lysosome diameter only slightly decreases speed. Overall, these results demonstrate the importance of decomposing particle trajectories into qualitatively different behaviors before conducting population-wide statistical analysis. Our results suggest that intracellular region is an important factor to consider in studies of intracellular transport.

A closer look at the spreaders of COVID-19 in Wisconsin and the US.

In this study, we design and use a mathematical model to primarily address the question of who are the main drivers of COVID-19 - the symptomatic infectious or the pre-symptomatic and asymptomatic infectious in the state of Wisconsin and the entire United States. To set the stage, we first briefly simulate and illustrate the benefit of lockdown. With these lockdown scenarios, and in general, the more dominant influence of the the pre-symptomatic and asymptomatic infectious over the symptomatic infectious, is shown in various ways. Numerical simulations for the U.S. show that an increase in testing and isolating for the pre-symptomatic and asymptomatic infectious group has up to 4 times more impact than an increase in testing for the symptomatic infectious in terms of cumulative deaths. An increase in testing for the pre-symptomatic and asymptomatic infectious group also has significantly more impact (on the order of twice as much) on reducing the control reproduction number than testing for symptomatic infectious. Lastly, we use our model to simulate an implementation of a natural herd immunity strategy for the entire U.S. and for the state of Wisconsin (once an epicenter for COVID-19). These simulations provide specific examples confirming that such a strategy requires a significant number of deaths before immunity is achieved, and as such, this strategy is certainly questionable in terms of success.