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Lysosomes are highly dynamic degradation/recycling organelles that harbor sophisticated molecular sensors and signal transduction machinery through which they control cell adaptation to environmental cues and nutrients. The movements of these signaling hubs comprise persistent, directional runs-active, ATP-dependent transport along the microtubule tracks-interspersed by short, passive movements and pauses imposed by cytoplasmic constraints. The trajectories of individual lysosomes are usually obtained by time-lapse imaging of the acidic organelles labeled with LysoTracker dyes or fluorescently-tagged lysosomal-associated membrane proteins LAMP1 and LAMP2. Subsequent particle tracking generates large data sets comprising thousands of lysosome trajectories and hundreds of thousands of data points. Analyzing such data sets requires unbiased, automated methods to handle large data sets while capturing the temporal heterogeneity of lysosome trajectory data. This chapter describes integrated and largely automated workflow from live cell imaging to lysosome trajectories to computing the parameters of lysosome dynamics. We describe an open-source code for implementing the continuous wavelet transform (CWT) to distinguish trajectory segments corresponding to active transport (i.e., "runs" and "flights") versus passive lysosome movements. Complementary cumulative distribution functions (CDFs) of the "runs/flights" are generated, and Akaike weight comparisons with several competing models (lognormal, power law, truncated power law, stretched exponential, exponential) are performed automatically. Such high-throughput analyses yield useful aggregate/ensemble metrics for lysosome active transport.

AlphaFold2 (AF) is a promising tool, but is it accurate enough to predict single mutation effects? Here, we report that a measure for localized structural deformation between protein pairs differing by only 1-3 mutations is correlated across 4,645 experimental and AF-predicted structures. Furthermore, analysis of ∼10,000 proteins shows that the local structural change correlates with various phenotypic changes. These findings suggest that AF can predict the magnitude of single-mutation effects in many proteins, and we propose a method to identify those proteins for which AF is predictive.

This work describes granular crystals held together by unusual, multipolar interactions and, under the application of an external bias, undergoing reversible structural transitions between closed and open forms. The system comprises two types of polymeric beads agitated on one or between two conductive plates and gradually acquiring charges by contact electrification. The charges thus developed induce a series of electrostatic images in the conductive supports and, in effect, the beads interact via dipolar or multipolar interactions, enabling the stabilization of non-electroneutral crystals. Furthermore, under an applied bias, the beads become polarized and their complex interactions (due to the series of image charges as well as series of image dipoles) result in open-pore crystals which return to compact forms upon bias removal. These effects are rationalized by analytical calculations, and the crystal structures observed in the experiments are reproduced by molecular dynamics simulations.

Metastatic cancer cells differ from their non-metastatic counterparts not only in terms of molecular composition and genetics, but also by the very strategy they employ for locomotion. Here, we analyzed large-scale statistics for cells migrating on linear microtracks to show that metastatic cancer cells follow a qualitatively different movement strategy than their non-invasive counterparts. The trajectories of metastatic cells display clusters of small steps that are interspersed with long “flights”. Such movements are characterized by heavy-tailed, truncated power law distributions of persistence times and are consistent with the Lévy walks that are also often employed by animal predators searching for scarce prey or food sources. In contrast, non-metastatic cancerous cells perform simple diffusive movements. These findings are supported by preliminary experiments with cancer cells migrating away from primary tumors in vivo. The use of chemical inhibitors targeting actin-binding proteins allows for “reprogramming” the Lévy walks into either diffusive or ballistic movements.

Placed at a water/air interface, particles of porphyrin-based MOFs (metal–organic frameworks) cut from large-area films display efficient, multiple-use autonomous motility powered by release of solvents incorporated in the MOF matrix and directionality dictated by their shapes. The particles can be refueled multiple times and can achieve speeds of ca. 200 mm·s–1 with high kinetic energy per unit of chemical “fuel” expended (>50 μJ·g–1). Efficiency of motion depends on the nature of the fuel used as well as the microstructure and surface wettability of the MOF surface. When multiple movers are present at the interface, they organize into “open” structures that exhibit collective, time-periodic motions.