Polaritonic molecular clock for all-optical ultrafast imaging of wavepacket dynamics without probe pulses

Conventional approaches to probing ultrafast molecular dynamics rely on the use of synchronized laser pulses with a well-defined time delay. Typically, a pump pulse excites a molecular wavepacket. A subsequent probe pulse can then dissociate or ionize the molecule, and measurement of the molecular fragments provides information about where the wavepacket was for each time delay. Here, we propose to exploit the ultrafast nuclear-position-dependent emission obtained due to large light–matter coupling in plasmonic nanocavities to image wavepacket dynamics using only a single pump pulse. We show that the time-resolved emission from the cavity provides information about when the wavepacket passes a given region in nuclear configuration space. This approach can image both cavity-modified dynamics on polaritonic (hybrid light–matter) potentials in the strong light–matter coupling regime and bare-molecule dynamics in the intermediate coupling regime of large Purcell enhancements, and provides a route towards ultrafast molecular spectroscopy with plasmonic nanocavitiesThis work has been funded by the European Research Council grant ERC-2016-STG-714870 and the Spanish Ministry for Science, Innovation, and Universities—AEI grants RTI2018-099737-B-I00, PCI2018-093145 (through the QuantERA program of the European Commission), and CEX2018-000805-M (through the María de Maeztu program for Units of Excellence in R&D

Three-Dimensional and Chemical Mapping of Intracellular Signaling Nanodomains in Health and Disease with Enhanced Expansion Microscopy

Nanodomains are intracellular foci which transduce signals between major cellular compartments. One of the most ubiquitous signal transducers, the ryanodine receptor (RyR) calcium channel, is tightly clustered within these nanodomains. Super-resolution microscopy has previously been used to visualize RyR clusters near the cell surface. A majority of nanodomains located deeper within cells have remained unresolved due to limited imaging depths and axial resolution of these modalities. A series of enhancements made to expansion microscopy allowed individual RyRs to be resolved within planar nanodomains at the cell periphery and the curved nanodomains located deeper within the interiors of cardiomyocytes. With a resolution of ∼ 15 nm, we localized both the position of RyRs and their individual phosphorylation for the residue Ser2808. With a three-dimensional imaging protocol, we observed disturbances to the RyR arrays in the nanometer scale which accompanied right-heart failure caused by pulmonary hypertension. The disease coincided with a distinct gradient of RyR hyperphosphorylation from the edge of the nanodomain toward the center, not seen in healthy cells. This spatial profile appeared to contrast distinctly from that sustained by the cells during acute, physiological hyperphosphorylation when they were stimulated with a β-adrenergic agonist. Simulations of RyR arrays based on the experimentally determined channel positions and phosphorylation signatures showed how the nanoscale dispersal of the RyRs during pathology diminishes its intrinsic likelihood to ignite a calcium signal. It also revealed that the natural topography of RyR phosphorylation could offset potential heterogeneity in nanodomain excitability which may arise from such RyR reorganization

A genomic catalog of Earth’s microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes