Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences.

The idea that liquid-liquid phase separation (LLPS) may be a general mechanism by which molecules in the complex cellular milieu may self-organize has generated much excitement and fervor in the cell biology community. While this concept is not new, its rise to preeminence has resulted in renewed interest in the mechanisms that shape and drive diverse cellular self-assembly processes from gene expression to cell division to stress responses. In vitro biochemical data have been instrumental in deriving some of the fundamental principles and molecular grammar by which biological molecules may phase separate, and the molecular basis of these interactions. Definitive evidence is lacking as to whether the same principles apply in the physiological environment inside living cells. In this Perspective, we analyze the evidence supporting phase separation in vivo across multiple cellular processes. We find that the evidence for in vivo LLPS is often phenomenological and inadequate to discriminate between phase separation and other possible mechanisms. Moreover, the causal relationship and functional consequences of LLPS in vivo are even more elusive. We underscore the importance of performing quantitative measurements on proteins in their endogenous state and physiological abundance, as well as make recommendations for experiments that may yield more conclusive results.

A Highly Accurate Pixel-Based FRAP Model Based on Spectral-Domain Numerical Methods.

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.

[Parameters which affect the estimation of protein mobility by method FRAP in living cells on the example of protein fibrillarin].

Method FRAP (fluorescence recovery after photobleaching) in combination with confocal laser scanning microscopy represents one of the principal approaches in studying the properties of proteins in living mammal cells. However, the data of different authors on the dynamic properties of the same protein and even in cells of the same type can differ greatly. The reasons of such discrepancies were not specifically analyzed yet. In the present work, on the example of the nucleolar protein fibrillarin fused to EGFP, was studied the impact of area of the region of interest (ROI) and temperature conditions on the main dynamic characteristics of the protein, such as mobile fraction and time for half-time of fluorescence recovery after photobleaching (t1/2). Obtained results suggest that both parameters have a great impact on the estimation of mobile properties of fibrillarin-EGFP in HeLa cells. Was concluded that during FRAP experiments the area of ROI has to be standardized and, as possible, minimized. Moreover, analyzing the dynamic properties of the nucleolar proteins, which take part in the temperature-sensitive reactions, the standard temperature conditions should also be standardized.

Dietary antioxidants interfere with Amplex Red-coupled-fluorescence assays.

Oxidation of Amplex Red by hydrogen peroxide in the presence of horseradish peroxidase (HRP) gives rise to an intensely colour product, resorufin. This reaction has been frequently employed for measurements based on enzyme-coupled reactions that detect hydrogen peroxide as a final reaction product. In the current study, we show that the presence of dietary antioxidants at biological concentrations in the reaction medium produced interferences in the Amplex Red/HRP catalyzed reaction that result in an over quantification of the hydrogen peroxide produced. The interference observed showed a dose-dependent manner, and a possible mechanism of interaction of dietary antioxidants with HRP in the Amplex Red-coupled-fluorescent assay is proposed.

MRT letter: high speed scanning has the potential to increase fluorescence yield and to reduce photobleaching.

True confocal microscopy requires point-shaped illumination and detection. To generate an image, a diffraction limited spot is moved over the sample. Single spot scanning has suffered in the past from low image rates; a solution is the employment of very fast scanning devices (resonant scanners) for x-movement. In the process of introducing resonant scanning devices, it was found that both signal yield is improved and bleaching is decreased-in contrary to the assumed performance. This article will show by a simple and well understood model a straightforward explanation for the potential increase of signal yield and decrease in photobleaching. The time that is ruling the dose-rate effects is the effective time; a fluorochrome is illuminated. This time depends on the diameter of the spot that is moved over the sample and the speed at which the spot moves. In essence, the scan process causes a pulsed illumination of the fluorochromes. Various schemes of pulsed illumination are simulated with a fluorescence model. The model includes a dark state, where fluorochromes will exit the fluorescence process and slowly decay back into the ground state. Upon splitting a single dose into two pulses separated by a dark time-reflecting an increased scan speed-the amount of fluorescence emission is increased and bleaching is reduced. These results show a potential increase of fluorescence and a lower photobleaching upon higher scan speed. As illumination during the bleach-phase in a FRAP-experiment is similar to a light pulse, the findings also suggest to critically consider the very beginning of fluorescence recovery in terms of triplet relaxation process that potentially could falsify the measurements.

Determining absolute protein numbers by quantitative fluorescence microscopy.

Biological questions are increasingly being addressed using a wide range of quantitative analytical tools to examine protein complex composition. Knowledge of the absolute number of proteins present provides insights into organization, function, and maintenance and is used in mathematical modeling of complex cellular dynamics. In this chapter, we outline and describe three microscopy-based methods for determining absolute protein numbers--fluorescence correlation spectroscopy, stepwise photobleaching, and ratiometric comparison of fluorescence intensity to known standards. In addition, we discuss the various fluorescently labeled proteins that have been used as standards for both stepwise photobleaching and ratiometric comparison analysis. A detailed procedure for determining absolute protein number by ratiometric comparison is outlined in the second half of this chapter. Counting proteins by quantitative microscopy is a relatively simple yet very powerful analytical tool that will increase our understanding of protein complex composition.