Exploring generic principles of compartmentalization in a developmental in vitro model.

Self-organization of cells into higher-order structures is key for multicellular organisms, for example via repetitive replication of template-like founder cells or syncytial energids. Yet, very similar spatial arrangements of cell-like compartments ('protocells') are also seen in a minimal model system of Xenopus egg extracts in the absence of template structures and chromatin, with dynamic microtubule assemblies driving the self-organization process. Quantifying geometrical features over time, we show here that protocell patterns are highly organized with a spatial arrangement and coarsening dynamics similar to that of two-dimensional foams but without the long-range ordering expected for hexagonal patterns. These features remain invariant when enforcing smaller protocells by adding taxol, i.e. patterns are dominated by a single, microtubule-derived length scale. Comparing our data to generic models, we conclude that protocell patterns emerge by simultaneous formation of randomly assembling protocells that grow at a uniform rate towards a frustrated arrangement before fusion of adjacent protocells eventually drives coarsening. The similarity of protocell patterns to arrays of energids and cells in developing organisms, but also to epithelial monolayers, suggests generic mechanical cues to drive self-organized space compartmentalization.

Quantifying active diffusion in an agitated fluid.

Mixing of reactants in microdroplets predominantly relies on diffusional motion due to small Reynolds numbers and the resulting absence of turbulent flows. Enhancing diffusion in microdroplets by an auxiliary noise source is therefore a topical problem. Here we report on how the diffusional motion of tracer beads is enhanced upon agitating the surrounding aqueous fluid with miniaturized magnetic stir bars that are compatible with microdroplets and microfluidic devices. Using single-particle tracking, we demonstrate via a broad palette of measures that local stirring of the fluid at different frequencies leads to an enhanced but apparently normal and homogenous diffusion process, i.e. diffusional steps follow the anticipated Gaussian distribution and no ballistic motion is observed whereas diffusion coefficients are significantly increased. The signature of stirring is, however, visible in the power-spectral density and in the velocity autocorrelation function of trajectories. Our data therefore demonstrate that diffusive mixing can be locally enhanced with miniaturized stir bars while only moderately affecting the ambient noise properties. The latter may also facilitate the controlled addition of nonequilibrium noise to complex fluids in future applications.

Miniaturized magnetic stir bars for controlled agitation of aqueous microdroplets.

Controlled stirring of tiny volumes of aqueous fluids is of particular importance in the life sciences, e.g. in the context of microfluidic and lab-on-chip applications. Local stirring not only accelerates fluid mixing and diffusion-limited processes, but it also allows for adding controlled active noise to the fluid. Here we report on the synthesis and characterization of magnetic nano-stir bars (MNBs) with which these features can be achieved in a straightforward fashion. We also demonstrate the applicability of MNBs to cell extract droplets in microfluidic channels and we show that they can introduce active noise to cell extracts as evidenced by altered fluctuations of ensembles of cytoskeletal filaments.