SummaryAccurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding of tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, and open source computational methods. Using DLP+, we have generated a resource of 51,926 single-cell genomes and matched cell images from diverse cell types including cell lines, xenografts, and diagnostic samples with limited material. From this resource we have defined variation in mitotic mis-segregation rates across tissue types and genotypes. Analysis of matched genomic and image measurements revealed correlations between cellular morphology and genome ploidy states. Aggregation of cells sharing copy number profiles allowed for calculation of single-nucleotide resolution clonal genotypes and inference of clonal phylogenies and avoided the limitations of bulk deconvolution. Finally, joint analysis over the above features defined clone-specific chromosomal aneuploidy in polyclonal populations.

We provide evidence that the chirality of collagen can give rise to strong second-harmonic generation circular dichroism (SHG-CD) responses in nonlinear microscopy. Although chirality is an intrinsic structural property of collagen, most of the previous studies ignore that property. We demonstrate chiral imaging of individual collagen fibers by using a laser scanning microscope and type-I collagen from pig ligaments. 100% contrast level of SHG-CD is achieved with sub-micrometer spatial resolution. As a new contrast mechanism for imaging chiral structures in bio-tissues, this technique provides information about collagen morphology and three-dimensional orientation of collagen molecules.

The decomposition of methanol catalyzed with Rh nanoclusters supported on an ordered thin film of Al2O3/NiAl­(100) became enhanced on decreasing the size of the clusters. The decomposition of methanol (and methanol-d 4) proceeded through dehydrogenation; the formation thereby of CO became evident above 200 K, depending little on the cluster size. In contrast, the production of CO and hydrogen (deuterium) from the reaction varied notably with the cluster size. The quantity of either CO or hydrogen produced per Rh surface site was unaltered on clusters of diameter >1.5 nm and height >0.6 nm, corresponding to about 65% of methanol undergoing decomposition on adsorption in a monolayer on the clusters. For clusters of diameter <1.5 nm and height <0.6 nm, the production per Rh surface site increased with decreasing size, up to 4 times that on the large clusters or Rh(100) single-crystal surface. The reactivity was enhanced largely because, with decreasing cluster size, the activation energy for the scission of the O–H bond in the initial dehydrogenation became smaller than the activation energy for the competing desorption. The property was associated with the edge Rh atoms at the surface of small clusters.

We show that scattering from a single gold nanoparticle is saturable for the first time. Wavelength-dependent study reveals that the saturation behavior is governed by depletion of surface plasmon resonance, not the thermal effect. We observed interesting flattening of the point spread function of scattering from a single nanoparticle due to saturation. By extracting the saturated part of scattering via temporal modulation, we achieve λ/8 point spread function in far-field imaging with unambiguous separation of adjacent particles.

Nonlinear optical interaction is crucial to alloptical signal processing. In metallic nanostructures, both linear and nonlinear optical interactions can be greatly enhanced by surface plasmon resonance (SPR). In the last few decades, saturation and reverse saturation of absorption in plasmonic materials have been unraveled. It is known that scattering is one of the fundamental light−matter interactions and is particularly strong in metallic nanoparticles due to SPR. However, previous methods measure response from ensemble of nanoparticles and did not characterize scattering on a single particle basis. Here we report that backscattering from an isolated gold nanoparticle exhibits not only saturation, but also reverse saturation. Wavelength-dependent and intensitydependent studies reveal that nonlinear scattering is dominated by SPR and shares a similar physical origin with nonlinear absorption. The reversibility and repeatability of saturable scattering (SS) and reverse saturable scattering (RSS) are validated via repetitive excitation on the same set of particles. Compared to fluorescence, our novel discovery of single-particle-based SS and RSS does not suffer from bleaching and can be used as a more robust contrast agent for optical microscopy. Under a reflection confocal microscope, interesting point-spread functions are observed, with full-width-of-half-maximum of central and side lobes reduced to λ/5 and λ/13, showing great potential for superresolution microscopy.