SUMMARY Stress granules are mRNA-protein granules that form when translation initiation is limited and are related to pathological granules in various neurodegenerative diseases. Super-resolution microscopy reveals stable substructures referred to as cores within stress granules that can be purified. Proteomic analysis of stress granule cores reveals a dense network of protein-protein interactions, links between stress granules and human diseases, and identifies ATP-dependent helicases and protein remodelers as conserved stress granule components. ATP is required for stress granule assembly and dynamics. Moreover, multiple ATP-driven machines affect stress granules differently; with the CCT complex inhibiting stress granule assembly, while the MCM and RVB complexes promote stress granule persistence. Our observations suggest that stress granules contain a stable core structure surrounded by a dynamic shell with assembly, disassembly and transitions between the core and shell modulated by numerous protein and RNA remodeling complexes.

When a single molecule is detected in a wide-field microscope, the image approximates the point spread function of the system. However, as the distribution of molecules becomes denser and their images begin to overlap, existing solutions to determine the number of molecules present and their precise three-dimensional locations can tolerate little to no overlap. We propose a localization scheme that can identify several overlapping molecule images while maintaining high localization precision. A solution to this problem involving matched optical and digital techniques, as here proposed, can substantially increase the allowable labeling density and accelerate the data collection time of single-molecule localization microscopy by more than one order of magnitude.

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We propose a super-resolution technique for dense clusters of blinking emitters. The method relies on two basic assumptions: the emitters are statistically independent and a model of the imaging system is known. We numerically analyze the performance limits of the method as a function of emitter density and noise level. Numerical simulations show that five closely packed emitters can be resolved and localized to a precision of 17 nm. The experimental resolution of five quantum dots located within a diffraction-limited spot confirms the applicability of this approach. Statistical tests validate the independence of our quantum dots separated by nanoscale distances.

A compact planar channel four-port drop filter is developed experimentally and theoretically in the three-dimensional woodpile photonic crystal having a complete band gap. This consists of two waveguides separated by a defect in a single layer of the photonic crystal. Frequencies for channel dropping can be tuned throughout the band gap, by changing the size of the defect. Quality factors of approximately 1000 were measured. Simulations demonstrate directional energy transfer between the input and out put waveguides, through excitation of fields in the defect region. The planar nature of the filter is much more amenable to fabrication at optical length wavelengths.