Person:

Park, Hongkun

We demonstrate a method of imaging spatially varying magnetic fields using a thin layer of nitrogen-vacancy (NV) centers at the surface of a diamond chip. Fluorescence emitted by the two-dimensional NV ensemble is detected by a CCD array, from which a vector magnetic field pattern is reconstructed. As a demonstration, ac current is passed through wires placed on the diamond chip surface, and the resulting ac magnetic field patterns are imaged using an echo-based technique with sub-micron resolution over a (140 \mu m) x (140 \mu m) field of view, giving single-pixel sensitivity (\sim 100 nT / \sqrt{Hz}). We discuss ongoing efforts to further improve the sensitivity, as well as potential bioimaging applications such as real-time imaging of activity in functional, cultured networks of neurons.

Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the regulatory mechanisms that facilitate cellular transitions in a human context. To that end, we performed comprehensive transcriptional and epigenetic profiling of populations derived through directed differentiation of hESCs representing each of the three embryonic germ layers. Integration of whole-genome bisulfite sequencing, chromatin immunoprecipitation sequencing, and RNA sequencing reveals unique events associated with specification toward each lineage. Lineage-specific dynamic alterations in DNA methylation and H3K4me1 are evident at putative distal regulatory elements that are frequently bound by pluripotency factors in the undifferentiated hESCs. In addition, we identified germ-layer-specific H3K27me3 enrichment at sites exhibiting high DNA methylation in the undifferentiated state. A better understanding of these initial specification events will facilitate identification of deficiencies in current approaches, leading to more faithful differentiation strategies as well as providing insights into the rewiring of human regulatory programs during cellular transitions.

Despite their importance, the molecular circuits that control the differentiation of naïve 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 nanowire-based tools for performing perturbations in primary T cells to systematically derive and experimentally validate a model of the dynamic regulatory network that controls Th17 differentiation. The network consists of two self-reinforcing, but mutually antagonistic, modules, with 12 novel regulators, whose coupled action may be essential for maintaining the balance between Th17 and other CD4+ T cell subsets. Overall, our study identifies and validates 39 regulatory factors, embeds them within a comprehensive temporal network and reveals its organizational principles, and highlights novel drug targets for controlling Th17 differentiation.

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 (DCs) spanning several experimental conditions. We find substantial variation between identically stimulated DCs, in both the fraction of cells detectably expressing a given mRNA 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, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analyzing DCs from knockout mice, and modulating secretion and extracellular signaling, we show that this response is coordinated via interferon-mediated paracrine signaling. Surprisingly, preventing cell-to-cell communication also substantially reduces variability in the expression of an early-induced “peaked” inflammatory module, suggesting that paracrine signaling 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 use to establish complex dynamic responses.

We describe and experimentally demonstrate a technique for deterministic, large coupling between a photonic crystal (PC) nanocavity and single photon emitters. The technique is based on in situ scanning of a PC cavity over a sample and allows the precise positioning of the cavity over a desired emitter with nanoscale resolution. The power of the technique is demonstrated by coupling the PC nanocavity to a single nitrogen vacancy (NV) center in diamond, an emitter system that provides optically accessible electron and nuclear spin qubits.

Photonic circuits can be much faster than their electronic counterparts, but they are difficult to miniaturize below the optical wavelength scale. Nanoscale photonic circuits based on surface plasmon polaritons (SPPs) are a promising solution to this problem because they can localize light below the diffraction limit. However, there is a general trade-off between the localization of an SPP and the efficiency with which it can be detected with conventional far-field optics. Here, we describe a new all-electrical SPP detection technique based on the near-field coupling between guided plasmons and a nanowire field-effect transistor. We use the technique to electrically detect the plasmon emission from an individual colloidal quantum dot coupled to an SPP waveguide. Our detectors are both nanoscale and highly efficient (0.1 electrons per plasmon), and a plasmonic gating effect can be used to amplify the signal even higher (up to 50 electrons per plasmon). These results may enable new on-chip optical sensing applications and are a key step towards 'dark' optoplasmonic nanocircuits in which SPPs can be generated, manipulated and detected without involving far-field radiation.

Recent molecular studies have revealed that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels, and phenotypic output1–5, with important functional consequences4,5. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs1,2 or proteins5,6 simultaneously because genomic profiling methods3 could not be applied to single cells until very recently7–10. Here, we use single-cell RNA-Seq to investigate heterogeneity in the response of bone marrow derived dendritic cells (BMDCs) to lipopolysaccharide (LPS). We find extensive, and previously unobserved, bimodal variation in mRNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization (RNA-FISH) 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.

We propose and demonstrate a new approach for achieving enhanced light-matter interactions with quantum emitters. Our approach makes use of a plasmon resonator composed of defect-free, highly crystalline silver nanowires surrounded by patterned dielectric distributed Bragg reflectors. These resonators have an effective mode volume (Veff) 2 orders of magnitude below the diffraction limit and a quality factor (Q) approaching 100, enabling enhancement of spontaneous emission rates by a factor exceeding 75 at the cavity resonance. We also show that these resonators can be used to convert a broadband quantum emitter to a narrow-band single-photon source with color-selective emission enhancement.

A variety of nanoscale photonic, mechanical, electronic, and optoelectronic devices require scalable thin film fabrication. Typically, the device layer is defined by thin film deposition on a substrate of a different material, and optical or electrical isolation is provided by the material properties of the substrate or by removal of the substrate. For a number of materials this planar approach is not feasible, and new fabrication techniques are required to realize complex nanoscale devices. Here, we report a three-dimensional fabrication technique based on anisotropic plasma etching at an oblique angle to the sample surface. As a proof of concept, this angled-etching methodology is used to fabricate free-standing nanoscale components in bulk single-crystal diamond, including nanobeam mechanical resonators, optical waveguides, and photonic crystal and microdisk cavities. Potential applications of the fabricated prototypes range from classical and quantum photonic devices to nanomechanical-based sensors and actuators.

Sensitive probing of temperature variations on nanometre scales is an outstanding challenge in many areas of modern science and technology. In particular, a thermometer capable of subdegree temperature resolution over a large range of temperatures as well as integration within a living system could provide a powerful new tool in many areas of biological, physical and chemical research. Possibilities range from the temperature-induced control of gene expression and tumour metabolism to the cell-selective treatment of disease and the study of heat dissipation in integrated circuits. By combining local light-induced heat sources with sensitive nanoscale thermometry, it may also be possible to engineer biological processes at the subcellular level. Here we demonstrate a new approach to nanoscale thermometry that uses coherent manipulation of the electronic spin associated with nitrogen–vacancy colour centres in diamond. Our technique makes it possible to detect temperature variations as small as 1.8 mK (a sensitivity of (9 mK Hz^{−1/2}) in an ultrapure bulk diamond sample. Using nitrogen–vacancy centres in diamond nanocrystals (nanodiamonds), we directly measure the local thermal environment on length scales as short as 200 nanometres. Finally, by introducing both nanodiamonds and gold nanoparticles into a single human embryonic fibroblast, we demonstrate temperature-gradient control and mapping at the subcellular level, enabling unique potential applications in life sciences.