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Author(s): David R. Glenn [1]; Dominik B. Bucher [1, 2]; Junghyun Lee [3]; Mikhail D. Lukin [1]; Hongkun Park [1, 4]; Ronald L. Walsworth (corresponding author) [1, 2] Quantum systems [...]

Metamaterials are artificial optical media composed of sub-wavelength metallic and dielectric building blocks that feature optical phenomena not present in naturally occurring materials [1-7]. Although they can serve as the basis for unique optical devices that mould the flow of light in unconventional ways, three-dimensional metamaterials suffer from extreme propagation losses [8,9]. Two-dimensional metamaterials (metasurfaces) such as hyperbolic metasurfaces for propagating surface plasmon polaritons (10,11) have the potential to alleviate this problem. Because the surface plasmon polaritons are guided at a metal-dielectric interface (rather than passing through metallic components), these hyperbolic metasurfaces have been predicted to suffer much lower propagation loss while still exhibiting optical phenomena akin to those in three-dimensional metamaterials. Moreover, because of their planar nature, these devices enable the construction of integrated metamaterial circuits as well as easy coupling with other optoelectronic elements. Here we report the experimental realization of a visible-frequency hyperbolic metasurface using single-crystal silver nanostructures defined by lithographic and etching techniques. The resulting devices display the characteristic properties of metamaterials, such as negative refraction (1-5) and diffraction-free propagation (6,7), with device performance greatly exceeding those of previous demonstrations. Moreover, hyperbolic metasurfaces exhibit strong, dispersion-dependent spin-orbit coupling, enabling polarization-and wavelength-dependent routeing of surface plasmon polaritons and two-dimensional chiral optical components (12-15). These results open the door to realizing integrated optical metacircuits, with wide-ranging applications in areas from imaging and sensing to quantum optics and quantum information science., Our approach for realizing a visible-frequency hyperbolic metasurface (HMS) involves the definition of a nanometre-scale silver/air grating on a sputter-deposited, single-crystalline silver film by electron-beam lithography and plasma etching. Unlike [...]

High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation between identically stimulated dendritic cells, in both the fraction of cells detectably expressing a given messenger RNA and the transcript's level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a 'core' module of antiviral genes is expressed very early by a few 'precocious' cells in response to uniform stimulation with a pathogenic component, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analysing dendritic cells from knockout mice, and modulating secretion and extracellular signalling, we show that this response is coordinated by interferon-mediated paracrine signalling from these precocious cells. Notably, preventing cell-to-cell communication also substantially reduces variability between cells in the expression of an early-induced 'peaked' inflammatory module, suggesting that paracrine signalling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations can use to establish complex dynamic responses., Variation in component molecules between individual cells (1-7) may have an important role in diversifying population-level responses (8-11), but also poses therapeutic challenges (4,5). Although pioneering studies have explored heterogeneity [...]

Single-cell RNA sequencing is used to investigate the transcriptional response of 18 mouse bone-marrow-derived dendritic cells after lipopolysaccharide stimulation; many highly expressed genes, such as key immune genes and cytokines, show bimodal variation in both transcript abundance and splicing patterns. This variation reflects differences in both cell state and usage of an interferon-driven pathway involving Stat2 and Irf7. Heterogeneity in immune cells Gene expression profiles are typically derived at cell-population level, yet there is growing evidence to suggest that seemingly identical individual cells can differ considerably in their gene expression. This paper describes the use of single-cell RNA sequencing (RNA-Seq) to analyse the transcriptional response of 18 mouse bone-marrow-derived dendritic cells after lipopolysaccharide stimulation. The authors find that even genes that are highly expressed at the population level -- such as key immune genes and cytokines -- are often bimodally expressed. They may be very highly expressed in one cell, and expressed hardly at all in another. This variation reflects differences in both cell state and usage of an interferon-driven pathway involving Stat2 and Irf7. The SMART-Seq technology used here could have wide application in the study of regulatory circuits at the single-cell level. Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output.sup.1,2,3,4,5, with important functional consequences.sup.4,5. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs.sup.1,2 or proteins.sup.5,6 simultaneously, because genomic profiling methods.sup.3 could not be applied to single cells until very recently.sup.7,8,9,10. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits., Author(s): Alex K. Shalek [sup.1] , Rahul Satija [sup.2] , Xian Adiconis [sup.2] , Rona S. Gertner [sup.1] , Jellert T. Gaublomme [sup.1] , Raktima Raychowdhury [sup.2] , Schraga Schwartz [...]

Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output (1-5), with important functional consequences (4,5). Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs (1,2) or proteins (5,6) simultaneously, because genomic profiling methods (3) could not be applied to single cells until very recently (7-10). Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits., To characterize the extent of expression variability on a genomic scale and decipher its functional implications, we used single-cell RNA sequencing (RNA-Seq) to profile a temporal snapshot of the BMDC [...]

Despite their importance, the molecular circuits that control the differentiation of naive T cells remain largely unknown. Recent studies that reconstructed regulatory networks in mammalian cells have focused on short-term responses and relied on perturbation-based approaches that cannot be readily applied to primary T cells. Here we combine transcriptional profiling at high temporal resolution, novel computational algorithms, and innovative nanowirebased perturbation tools to systematically derive and experimentally validate a model of the dynamic regulatory network that controls the differentiation of mouse [T.sub.H]17 cells, a proinflammatory T-cell subset that has been implicated in the pathogenesis of multiple autoimmune diseases. The [T.sub.H]17 transcriptional network consists of two self-reinforcing, but mutually antagonistic, modules, with 12 novel regulators, the coupled action of which may be essential for maintaining the balance between [T.sub.H]17 and other CD[4.sup.+] T-cell subsets. Our study identifies and validates 39 regulatory factors, embeds them within a comprehensive temporal network and reveals its organizational principles; it also highlights novel drug targets for controlling [T.sub.H]17 cell differentiation., Effective coordination of the immune system requires careful balancing of distinct pro-inflammatory and regulatory CD[4.sup.+] helper T-cell populations. Among those, pro-inflammatory IL-17 producing [T.sub.H]17 cells have a key role in [...]

A generalized platform for introducing a diverse range of biomolecules into living cells in high-throughput could transform how complex cellular processes are probed and analyzed. Here, we demonstrate spatially localized, efficient, and universal delivery of biomolecules into immortalized and primary mammalian cells using surface-modified vertical silicon nanowires. The method relies on the ability of the silicon nanowires to penetrate a cell's membrane and subsequently release surface-bound molecules directly into the cell's cytosol, thus allowing highly efficient delivery of biomolecules without chemical modification or viral packaging. This modality enables one to assess the phenotypic consequences of introducing a broad range of biological effectors (DNAs, RNAs, peptides, proteins, and small molecules) into almost any cell type. We show that this platform can be used to guide neuronal progenitor growth with small molecules, knock down transcript levels by delivering siRNAs, inhibit apoptosis using peptides, and introduce targeted proteins to specific organelles. We further demonstrate codelivery of siRNAs and proteins on a single substrate in a microarray format, highlighting this technology's potential as a robust, monolithic platform for high-throughput, miniaturized bioassays. doi/10.1073/pnas.0909350107

Author(s): Wenjie Liang [1]; Matthew P. Shores [2]; Marc Bockrath [1]; Jeffrey R. Long [2]; Hongkun Park (corresponding author) [1] When an individual molecule [1], nanocrystal [2, 3, 4], nanotube [...]

Author(s): Wenjie Liang [1, 2]; Marc Bockrath [2, 3]; Dolores Bozovic [3]; Jason H. Hafner [1]; M. Tinkham [3]; Hongkun Park (corresponding author) [1] The behaviour of traditional electronic devices [...]

Author(s): Hongkun Park [1, 3, 4]; Jiwoong Park [2]; Andrew K. L. Lim [1]; Erik H. Anderson [3]; A. Paul Alivisatos [1, 3]; Paul L. McEuen (corresponding author) [2, 3] [...]

Boron-doped silicon nanowires (SiNWs) were used to create highly sensitive, real-time electrically based sensors for biological and chemical species. Amine-and oxide-functionalized SiNWs exhibit pH-dependent conductance that was linear over a large dynamic range and could be understood in terms of the change in surface charge during protonation and deprotonation. Biotin-modified SiNWs were used to detect streptavidin down to at least a picomolar concentration range. In addition, antigen-functionalized SiNWs show reversible antibody binding and concentration-dependent detection in real time. Lastly, detection of the reversible binding of the metabolic indicator [Ca.sup.2+] was demonstrated. The small size and capability of these semiconductor nanowires for sensitive, label-free, real-time detection of a wide range of chemical and biological species could be exploited in array-based screening and in vivo diagnostics., Planar semiconductors can serve as the basis for chemical and biological sensors in which detection can be monitored electrically and/or optically (1-4). For example, a planar field effect transistor (FET) [...]

We report the characterization of defects in individual metallic single-walled carbon nanotubes by transport measurements and scanned gate microscopy. A sizable fraction of metallic nanotubes grown by chemical vapor deposition exhibits strongly gate voltage-dependent resistance at room temperature. Scanned gate measurements reveal that this behavior originates from resonant electron scattering by defects in the nanotube as the Fermi level is varied by the gate voltage. The reflection coefficient at the peak of a scattering resonance was determined to be about 0.5 at room temperature. An intratube quantum dot device formed by two defects is demonstrated by low-temperature transport measurements., Single-walled carbon nanotubes (SWNTs) have emerged as an attractive material for molecular electronic applications (1, 2). Depending on their diameter and chirality, SWNTs can be either one-dimensional metals or semiconductors, [...]