Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.

Extensive cellular heterogeneity exists within specific immune-cell subtypes classified as a single lineage, but its molecular underpinnings are rarely characterized at a genomic scale. Here, we use single-cell RNA-seq to investigate the molecular mechanisms governing heterogeneity and pathogenicity of Th17 cells isolated from the central nervous system (CNS) and lymph nodes (LN) at the peak of autoimmune encephalomyelitis (EAE) or differentiated in vitro under either pathogenic or non-pathogenic polarization conditions. Computational analysis relates a spectrum of cellular states in vivo to in-vitro-differentiated Th17 cells and unveils genes governing pathogenicity and disease susceptibility. Using knockout mice, we validate four new genes: Gpr65, Plzp, Toso, and Cd5l (in a companion paper). Cellular heterogeneity thus informs Th17 function in autoimmunity and can identify targets for selective suppression of pathogenic Th17 cells while potentially sparing non-pathogenic tissue-protective ones.

CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity.

Th17 cells play a critical role in host defense against extracellular pathogens and tissue homeostasis but can induce autoimmunity. The mechanisms implicated in balancing "pathogenic" and "non-pathogenic" Th17 cell states remain largely unknown. We used single-cell RNA-seq to identify CD5L/AIM as a regulator expressed in non-pathogenic, but not in pathogenic Th17 cells. Although CD5L does not affect Th17 differentiation, it is a functional switch that regulates the pathogenicity of Th17 cells. Loss of CD5L converts non-pathogenic Th17 cells into pathogenic cells that induce autoimmunity. CD5L mediates this effect by modulating the intracellular lipidome, altering fatty acid composition and restricting cholesterol biosynthesis and, thus, ligand availability for Rorγt, the master transcription factor of Th17 cells. Our study identifies CD5L as a critical regulator of the Th17 cell functional state and highlights the importance of lipid metabolism in balancing immune protection and disease induced by T cells.

Orbital multiferroicity in pentalayer rhombohedral graphene.

Ferroic orders describe spontaneous polarization of spin, charge and lattice degrees of freedom in materials. Materials exhibiting multiple ferroic orders, known as multiferroics, have important parts in multifunctional electrical and magnetic device applications1-4. Two-dimensional materials with honeycomb lattices offer opportunities to engineer unconventional multiferroicity, in which the ferroic orders are driven purely by the orbital degrees of freedom and not by electron spin. These include ferro-valleytricity corresponding to the electron valley5 and ferro-orbital-magnetism6 supported by quantum geometric effects. These orbital multiferroics could offer strong valley-magnetic couplings and large responses to external fields-enabling device applications such as multiple-state memory elements and electric control of the valley and magnetic states. Here we report orbital multiferroicity in pentalayer rhombohedral graphene using low-temperature magneto-transport measurements. We observed anomalous Hall signals Rxy with an exceptionally large Hall angle (tanΘH > 0.6) and orbital magnetic hysteresis at hole doping. There are four such states with different valley polarizations and orbital magnetizations, forming a valley-magnetic quartet. By sweeping the gate electric field E, we observed a butterfly-shaped hysteresis of Rxy connecting the quartet. This hysteresis indicates a ferro-valleytronic order that couples to the composite field E · B (where B is the magnetic field), but not to the individual fields. Tuning E would switch each ferroic order independently and achieve non-volatile switching of them together. Our observations demonstrate a previously unknown type of multiferroics and point to electrically tunable ultralow-power valleytronic and magnetic devices.

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.

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.

Bilayer Wigner crystals in a transition metal dichalcogenide heterostructure.

One of the first theoretically predicted manifestations of strong interactions in many-electron systems was the Wigner crystal1-3, in which electrons crystallize into a regular lattice. The crystal can melt via either thermal or quantum fluctuations4. Quantum melting of the Wigner crystal is predicted to produce exotic intermediate phases5,6 and quantum magnetism7,8 because of the intricate interplay of Coulomb interactions and kinetic energy. However, studying two-dimensional Wigner crystals in the quantum regime has often required a strong magnetic field9-11 or a moiré superlattice potential12-15, thus limiting access to the full phase diagram of the interacting electron liquid. Here we report the observation of bilayer Wigner crystals without magnetic fields or moiré potentials in an atomically thin transition metal dichalcogenide heterostructure, which consists of two MoSe2 monolayers separated by hexagonal boron nitride. We observe optical signatures of robust correlated insulating states at symmetric (1:1) and asymmetric (3:1, 4:1 and 7:1) electron doping of the two MoSe2 layers at cryogenic temperatures. We attribute these features to bilayer Wigner crystals composed of two interlocked commensurate triangular electron lattices, stabilized by inter-layer interaction16. The Wigner crystal phases are remarkably stable, and undergo quantum and thermal melting transitions at electron densities of up to 6 × 1012 per square centimetre and at temperatures of up to about 40 kelvin. Our results demonstrate that an atomically thin heterostructure is a highly tunable platform for realizing many-body electronic states and probing their liquid-solid and magnetic quantum phase transitions4-8,17.

Systematic discovery of TLR signaling components delineates viral-sensing circuits.

Deciphering the signaling networks that underlie normal and disease processes remains a major challenge. Here, we report the discovery of signaling components involved in the Toll-like receptor (TLR) response of immune dendritic cells (DCs), including a previously unkown pathway shared across mammalian antiviral responses. By combining transcriptional profiling, genetic and small-molecule perturbations, and phosphoproteomics, we uncover 35 signaling regulators, including 16 known regulators, involved in TLR signaling. In particular, we find that Polo-like kinases (Plk) 2 and 4 are essential components of antiviral pathways in vitro and in vivo and activate a signaling branch involving a dozen proteins, among which is Tnfaip2, a gene associated with autoimmune diseases but whose role was unknown. Our study illustrates the power of combining systematic measurements and perturbations to elucidate complex signaling circuits and discover potential therapeutic targets.

Operando electron microscopy investigation of polar domain dynamics in twisted van der Waals homobilayers.

Conventional antiferroelectric materials with atomic-scale anti-aligned dipoles undergo a transition to a ferroelectric (FE) phase under strong electric fields. The moiré superlattice formed in the twisted stacks of van der Waals crystals exhibits polar domains alternating in moiré length with anti-aligned dipoles. In this moiré domain antiferroelectic (MDAF) arrangement, the distribution of electric dipoles is distinguished from that of two-dimensional FEs, suggesting dissimilar domain dynamics. Here we performed an operando transmission electron microscopy investigation on twisted bilayer WSe2 to observe the polar domain dynamics in real time. We find that the topological protection, provided by the domain wall network, prevents the MDAF-to-FE transition. As one decreases the twist angle, however, this transition occurs as the domain wall network disappears. Exploiting stroboscopic operando transmission electron microscopy on the FE phase, we measure a maximum domain wall velocity of 300 µm s-1. Domain wall pinnings by various disorders limit the domain wall velocity and cause Barkhausen noises in the polarization hysteresis loop. Atomic-scale analysis of the pinning disorders provides structural insight on how to improve the switching speed of van der Waals FEs.

High-resolution magnetic resonance spectroscopy using a solid-state spin sensor.

Quantum systems that consist of solid-state electronic spins can be sensitive detectors of nuclear magnetic resonance (NMR) signals, particularly from very small samples. For example, nitrogen-vacancy centres in diamond have been used to record NMR signals from nanometre-scale samples, with sensitivity sufficient to detect the magnetic field produced by a single protein. However, the best reported spectral resolution for NMR of molecules using nitrogen-vacancy centres is about 100 hertz. This is insufficient to resolve the key spectral identifiers of molecular structure that are critical to NMR applications in chemistry, structural biology and materials research, such as scalar couplings (which require a resolution of less than ten hertz) and small chemical shifts (which require a resolution of around one part per million of the nuclear Larmor frequency). Conventional, inductively detected NMR can provide the necessary high spectral resolution, but its limited sensitivity typically requires millimetre-scale samples, precluding applications that involve smaller samples, such as picolitre-volume chemical analysis or correlated optical and NMR microscopy. Here we demonstrate a measurement technique that uses a solid-state spin sensor (a magnetometer) consisting of an ensemble of nitrogen-vacancy centres in combination with a narrowband synchronized readout protocol to obtain NMR spectral resolution of about one hertz. We use this technique to observe NMR scalar couplings in a micrometre-scale sample volume of approximately ten picolitres. We also use the ensemble of nitrogen-vacancy centres to apply NMR to thermally polarized nuclear spins and resolve chemical-shift spectra from small molecules. Our technique enables analytical NMR spectroscopy at the scale of single cells.

An Inverse-Designed Nanophotonic Interface for Excitons in Atomically Thin Materials.

Efficient nanophotonic devices are essential for applications in quantum networking, optical information processing, sensing, and nonlinear optics. Extensive research efforts have focused on integrating two-dimensional (2D) materials into photonic structures, but this integration is often limited by size and material quality. Here, we use hexagonal boron nitride (hBN), a benchmark choice for encapsulating atomically thin materials, as a waveguiding layer while simultaneously improving the optical quality of the embedded films. When combined with a photonic inverse design, it becomes a complete nanophotonic platform to interface with optically active 2D materials. Grating couplers and low-loss waveguides provide optical interfacing and routing, tunable cavities provide a large exciton-photon coupling to transition metal dichalcogenide (TMD) monolayers through Purcell enhancement, and metasurfaces enable the efficient detection of TMD dark excitons. This work paves the way for advanced 2D-material nanophotonic structures for classical and quantum nonlinear optics.

Robust Higher-Order Hamiltonian Engineering for Quantum Sensing with Strongly Interacting Systems.

Dynamical decoupling techniques constitute an integral part of many quantum sensing platforms, often leading to orders-of-magnitude improvements in coherence time and sensitivity. Most ac sensing sequences involve a periodic echolike structure, in which the target signal is synchronized with the echo period. We show that for strongly interacting systems, this construction leads to a fundamental sensitivity limit associated with imperfect interaction decoupling. We present a simple physical picture demonstrating the origin of this limitation, and further formalize these considerations in terms of concise higher-order decoupling rules. We then show how these limitations can be surpassed by identifying a novel sequence building block, in which the signal period matches twice the echo period. Using these decoupling rules and the resulting sequence building block, we experimentally demonstrate significant improvements in dynamical decoupling timescales and magnetic field sensitivity, opening the door for new applications in quantum sensing and quantum many-body physics.

Quantum Logic Enhanced Sensing in Solid-State Spin Ensembles.

We demonstrate quantum logic enhanced sensitivity for a macroscopic ensemble of solid-state, hybrid two-qubit sensors. We achieve over a factor of 30 improvement in the single-shot signal-to-noise ratio, translating to an ac magnetic field sensitivity enhancement exceeding an order of magnitude for time-averaged measurements. Using the electronic spins of nitrogen vacancy (NV) centers in diamond as sensors, we leverage the on-site nitrogen nuclear spins of the NV centers as memory qubits, in combination with homogeneous and stable bias and control fields, ensuring that all of the ∼10^{9} two-qubit sensors are sufficiently identical to permit global control of the NV ensemble spin states. We find quantum logic sensitivity enhancement for multiple measurement protocols with varying optimal sensing intervals, including XY8 and DROID-60 dynamical decoupling, as well as correlation spectroscopy, using an applied ac magnetic field signal. The results are independent of the nature of the target signal and broadly applicable to measurements using NV centers and other solid-state spin ensembles. This work provides a benchmark for macroscopic ensembles of quantum sensors that employ quantum logic or quantum error correction algorithms for enhanced sensitivity.

Controlling Local Thermalization Dynamics in a Floquet-Engineered Dipolar Ensemble.

Understanding the microscopic mechanisms of thermalization in closed quantum systems is among the key challenges in modern quantum many-body physics. We demonstrate a method to probe local thermalization in a large-scale many-body system by exploiting its inherent disorder and use this to uncover the thermalization mechanisms in a three-dimensional, dipolar-interacting spin system with tunable interactions. Utilizing advanced Hamiltonian engineering techniques to explore a range of spin Hamiltonians, we observe a striking change in the characteristic shape and timescale of local correlation decay as we vary the engineered exchange anisotropy. We show that these observations originate from the system's intrinsic many-body dynamics and reveal the signatures of conservation laws within localized clusters of spins, which do not readily manifest using global probes. Our method provides an exquisite lens into the tunable nature of local thermalization dynamics and enables detailed studies of scrambling, thermalization, and hydrodynamics in strongly interacting quantum systems.

Probing and manipulating embryogenesis via nanoscale thermometry and temperature control.

Understanding the coordination of cell-division timing is one of the outstanding questions in the field of developmental biology. One active control parameter of the cell-cycle duration is temperature, as it can accelerate or decelerate the rate of biochemical reactions. However, controlled experiments at the cellular scale are challenging, due to the limited availability of biocompatible temperature sensors, as well as the lack of practical methods to systematically control local temperatures and cellular dynamics. Here, we demonstrate a method to probe and control the cell-division timing in Caenorhabditis elegans embryos using a combination of local laser heating and nanoscale thermometry. Local infrared laser illumination produces a temperature gradient across the embryo, which is precisely measured by in vivo nanoscale thermometry using quantum defects in nanodiamonds. These techniques enable selective, controlled acceleration of the cell divisions, even enabling an inversion of division order at the two-cell stage. Our data suggest that the cell-cycle timing asynchrony of the early embryonic development in C. elegans is determined independently by individual cells rather than via cell-to-cell communication. Our method can be used to control the development of multicellular organisms and to provide insights into the regulation of cell-division timings as a consequence of local perturbations.

Modulation Doping of Single-Layer Semiconductors for Improved Contact at Metal Interfaces.

Single layers of two-dimensional (2D) materials hold the promise for further miniaturization of semiconductor electronic devices. However, the metal-semiconductor contact resistance limits device performance. To mitigate this problem, we propose modulation doping, specifically a doping layer placed on the opposite side of a metal-semiconductor interface. Using first-principles calculations to obtain the band alignment, we show that the Schottky barrier height and, consequently, the contact resistance at the metal-semiconductor interface can be reduced by modulation doping. We demonstrate the feasibility of this approach for a single-layer tungsten diselenide (WSe2) channel and 2D MXene modulation doping layers, interfaced with several different metal contacts. Our results indicate that the Fermi level of the metal can be shifted across the entire band gap. This approach can be straight-forwardly generalized for other 2D semiconductors and a wide variety of doping layers.

Excitons in a reconstructed moiré potential in twisted WSe2/WSe2 homobilayers.

Moiré superlattices in twisted van der Waals materials have recently emerged as a promising platform for engineering electronic and optical properties. A major obstacle to fully understanding these systems and harnessing their potential is the limited ability to correlate direct imaging of the moiré structure with optical and electronic properties. Here we develop a secondary electron microscope technique to directly image stacking domains in fully functional van der Waals heterostructure devices. After demonstrating the imaging of AB/BA and ABA/ABC domains in multilayer graphene, we employ this technique to investigate reconstructed moiré patterns in twisted WSe2/WSe2 bilayers and directly correlate the increasing moiré periodicity with the emergence of two distinct exciton species in photoluminescence measurements. These states can be tuned individually through electrostatic gating and feature different valley coherence properties. We attribute our observations to the formation of an array of two intralayer exciton species that reside in alternating locations in the superlattice, and open up new avenues to realize tunable exciton arrays in twisted van der Waals heterostructures, with applications in quantum optoelectronics and explorations of novel many-body systems.

Visible-frequency hyperbolic metasurface.

Metamaterials are artificial optical media composed of sub-wavelength metallic and dielectric building blocks that feature optical phenomena not present in naturally occurring materials. 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. Two-dimensional metamaterials (metasurfaces) such as hyperbolic metasurfaces for propagating surface plasmon polaritons 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 and diffraction-free propagation, 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. These results open the door to realizing integrated optical meta-circuits, with wide-ranging applications in areas from imaging and sensing to quantum optics and quantum information science.

Controlling Excitons in an Atomically Thin Membrane with a Mirror.

We demonstrate a new approach for dynamically manipulating the optical response of an atomically thin semiconductor, a monolayer of MoSe_{2}, by suspending it over a metallic mirror. First, we show that suspended van der Waals heterostructures incorporating a MoSe_{2} monolayer host spatially homogeneous, lifetime-broadened excitons. Then, we interface this nearly ideal excitonic system with a metallic mirror and demonstrate control over the exciton-photon coupling. Specifically, by electromechanically changing the distance between the heterostructure and the mirror, thereby changing the local photonic density of states in a controllable and reversible fashion, we show that both the absorption and emission properties of the excitons can be dynamically modulated. This electromechanical control over exciton dynamics in a mechanically flexible, atomically thin semiconductor opens up new avenues in cavity quantum optomechanics, nonlinear quantum optics, and topological photonics.

Electrically Tunable Valley Dynamics in Twisted WSe_{2}/WSe_{2} Bilayers.

The twist degree of freedom provides a powerful new tool for engineering the electrical and optical properties of van der Waals heterostructures. Here, we show that the twist angle can be used to control the spin-valley properties of transition metal dichalcogenide bilayers by changing the momentum alignment of the valleys in the two layers. Specifically, we observe that the interlayer excitons in twisted WSe_{2}/WSe_{2} bilayers exhibit a high (>60%) degree of circular polarization (DOCP) and long valley lifetimes (>40 ns) at zero electric and magnetic fields. The valley lifetime can be tuned by more than 3 orders of magnitude via electrostatic doping, enabling switching of the DOCP from ∼80% in the n-doped regime to <5% in the p-doped regime. These results open up new avenues for tunable chiral light-matter interactions, enabling novel device schemes that exploit the valley degree of freedom.

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

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.

The Design of a CMOS Nanoelectrode Array with 4096 Current-Clamp/Voltage-Clamp Amplifiers for Intracellular Recording/Stimulation of Mammalian Neurons.

CMOS microelectrode arrays (MEAs) can record electrophysiological activities of a large number of neurons in parallel but only extracellularly with low signal-to-noise ratio. Patch clamp electrodes can perform intracellular recording with high signal-to-noise ratio but only from a few neurons in parallel. Recently we have developed and reported a neuroelectronic interface that combines the parallelism of the CMOS MEA and the intracellular sensitivity of the patch clamp. Here, we report the design and characterization of the CMOS integrated circuit (IC), a critical component of the neuroelectronic interface. Fabricated in 0.18-µm technology, the IC features an array of 4,096 platinum black (PtB) nanoelectrodes spaced at a 20 µm pitch on its surface and contains 4,096 active pixel circuits. Each active pixel circuit, consisting of a new switched-capacitor current injector--capable of injecting from ±15 pA to ±0.7 µA with a 5 pA resolution--and an operational amplifier, is highly configurable. When configured into current-clamp mode, the pixel intracellularly records membrane potentials including subthreshold activities with ∼23 µVrms input referred noise while injecting a current for simultaneous stimulation. When configured into voltage-clamp mode, the pixel becomes a switched-capacitor transimpedance amplifier with ∼1 pArms input referred noise, and intracellularly records ion channel currents while applying a voltage for simultaneous stimulation. Such voltage/current-clamp intracellular recording/stimulation is a feat only previously possible with the patch clamp method. At the same time, as an array, the IC overcomes the lack of parallelism of the patch clamp method, measuring thousands of mammalian neurons in parallel, with full-frame intracellular recording/stimulation at 9.4 kHz.