Large-scale CRISPR screen reveals context-specific genetic regulation of retinal ganglion cell regeneration.

Many genes are known to regulate retinal regeneration following widespread tissue damage. Conversely, genes controlling regeneration following limited cell loss, per degenerative diseases, are undefined. As stem/progenitor cell responses scale to injury levels, understanding how the extent and specificity of cell loss impact regenerative processes is important. Here, transgenic zebrafish enabling selective retinal ganglion cell (RGC) ablation were used to identify genes that regulate RGC regeneration. A single cell multiomics-informed screen of 101 genes identified seven knockouts that inhibited and eleven that promoted RGC regeneration. Surprisingly, 35 of 36 genes known/implicated as being required for regeneration following widespread retinal damage were not required for RGC regeneration, and seven even enhanced regeneration kinetics, including proneural factors neurog1, olig2, and ascl1a. Mechanistic analyses revealed ascl1a disruption increased the propensity of progenitor cells to produce RGCs; i.e., increased "fate bias". These data demonstrate plasticity in how Müller glia can convert to a stem-like state and context-specificity in how genes function during regeneration. Increased understanding of how the regeneration of disease-relevant cell types is specifically controlled will support the development of disease-tailored regenerative therapeutics.

Evidence for electron-hole crystals in a Mott insulator.

The coexistence of correlated electron and hole crystals enables the realization of quantum excitonic states, capable of hosting counterflow superfluidity and topological orders with long-range quantum entanglement. Here we report evidence for imbalanced electron-hole crystals in a doped Mott insulator, namely, α-RuCl3, through gate-tunable non-invasive van der Waals doping from graphene. Real-space imaging via scanning tunnelling microscopy reveals two distinct charge orderings at the lower and upper Hubbard band energies, whose origin is attributed to the correlation-driven honeycomb hole crystal composed of hole-rich Ru sites and rotational-symmetry-breaking paired electron crystal composed of electron-rich Ru-Ru bonds, respectively. Moreover, a gate-induced transition of electron-hole crystals is directly visualized, further corroborating their nature as correlation-driven charge crystals. The realization and atom-resolved visualization of imbalanced electron-hole crystals in a doped Mott insulator opens new doors in the search for correlated bosonic states within strongly correlated materials.

Highly Selective On-Surface Ring-Opening of Aromatic Azulene Moiety.

Controllable ring-opening of polycyclic aromatic hydrocarbons plays a crucial role in various chemical and biological processes. However, breaking down aromatic covalent C-C bonds is exceptionally challenging due to their high stability and strong aromaticity. This study presents a seminal report on the precise and highly selective on-surface ring-opening of the seven-membered ring within the aromatic azulene moieties under mild conditions. The chemical structures of the resulting products were identified using bond-resolved scanning probe microscopy. Furthermore, through density functional theory calculations, we uncovered the mechanism behind the ring-opening process and elucidated its chemical driving force. The key to achieving this ring-opening process lies in manipulating the local aromaticity of the aromatic azulene moiety through strain-induced internal ring rearrangement and cyclodehydrogenation. By precisely controlling these factors, we successfully triggered the desired ring-opening reaction. Our findings not only provide valuable insights into the ring-opening process of polycyclic aromatic hydrocarbons but also open up new possibilities for the manipulation and reconstruction of these important chemical structures.

Air-Stable Wafer-Scale Ferromagnetic Metallo-Carbon Nitride Monolayer.

The pursuit of robust, long-range magnetic ordering in two-dimensional (2D) materials holds immense promise for driving technological advances. However, achieving this goal remains a grand challenge due to enhanced quantum and thermal fluctuations as well as chemical instability in the 2D limit. While magnetic ordering has been realized in atomically thin flakes of transition metal chalcogenides and metal halides, these materials often suffer from air instability. In contrast, 2D carbon-based materials are stable enough, yet the challenge lies in creating a high density of local magnetic moments and controlling their long-range magnetic ordering. Here, we report a novel wafer-scale synthesis of an air-stable metallo-carbon nitride monolayer (MCN, denoted as MN4/CNx), featuring ultradense single magnetic atoms and exhibiting robust room-temperature ferromagnetism. Under low-pressure chemical vapor deposition conditions, thermal dehydrogenation and polymerization of metal phthalocyanine (MPc) on copper foil at elevated temperature generate a substantial number of nitrogen coordination sites for anchoring magnetic single atoms in monolayer MN4/CNx (where M = Fe, Co, and Ni). The incorporation of densely populating MN4 sites into monolayer MCN networks leads to robust ferromagnetism up to room temperature, enabling the observation of anomalous Hall effects with excellent chemical stability. Detailed electronic structure calculations indicate that the presence of high-density metal sites results in the emergence of spin-split d-bands near the Fermi level, causing a favorable long-range ferromagnetic exchange coupling through direct exchange interactions. Our work demonstrates a novel synthesis approach for wafer-scale MCN monolayers with robust room-temperature ferromagnetism and may shed light on practical electronic and spintronic applications.

CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server.

MOTIVATION: Single-cell sequencing technology has become a routine in studying many biological problems. A core step of analyzing single-cell data is the assignment of cell clusters to specific cell types. Reference-based methods are proposed for predicting cell types for single-cell clusters. However, the scalability and lack of preprocessed reference datasets prevent them from being practical and easy to use. RESULTS: Here, we introduce a reference-based cell annotation web server, CellAnn, which is super-fast and easy to use. CellAnn contains a comprehensive reference database with 204 human and 191 mouse single-cell datasets. These reference datasets cover 32 organs. Furthermore, we developed a cluster-to-cluster alignment method to transfer cell labels from the reference to the query datasets, which is superior to the existing methods with higher accuracy and higher scalability. Finally, CellAnn is an online tool that integrates all the procedures in cell annotation, including reference searching, transferring cell labels, visualizing results, and harmonizing cell annotation labels. Through the user-friendly interface, users can identify the best annotation by cross-validating with multiple reference datasets. We believe that CellAnn can greatly facilitate single-cell sequencing data analysis. AVAILABILITY AND IMPLEMENTATION: The web server is available at www.cellann.io, and the source code is available at https://github.com/Pinlyu3/CellAnn_shinyapp.

A Fast Self-Calibration Method for Dual-Axis Rotational Inertial Navigation Systems Based on Invariant Errors.

In order to ensure that dual-axis rotational inertial navigation systems (RINSs) maintain a high level of accuracy over the long term, there is a demand for periodic calibration during their service life. Traditional calibration methods for inertial measurement units (IMUs) involve removing the IMU from the equipment, which is a laborious and time-consuming process. Reinstalling the IMU after calibration may introduce new installation errors. This paper focuses on dual-axis rotational inertial navigation systems and presents a system-level self-calibration method based on invariant errors, enabling high-precision automated calibration without the need for equipment disassembly. First, navigation parameter errors in the inertial frame are expressed as invariant errors. This allows the corresponding error models to estimate initial attitude even more rapidly and accurately in cases of extreme misalignment, eliminating the need for coarse alignment. Next, by utilizing the output of a gimbal mechanism, angular velocity constraint equations are established, and the backtracking navigation is introduced to reuse sensor data, thereby reducing the calibration time. Finally, a rotation scheme for the IMU is designed to ensure that all errors are observable. The observability of the system is analyzed based on a piecewise constant system method and singular value decomposition (SVD) observability analysis. The simulation and experimental results demonstrate that this method can effectively estimate IMU errors and installation errors related to the rotation axis within 12 min, and the estimated error is less than 4%. After using this method to compensate for the calibration error, the velocity and position accuracies of a RINS are significantly improved.

Periodic Distributions and Ultrafast Dynamics of Hot Electrons in Plasmonic Resonators.

Understanding and managing hot electrons in metals are of fundamental and practical interest in plasmonic studies and applications. A major challenge for the development of hot electron devices requires the efficient and controllable generation of long-lived hot electrons so that they can be harnessed effectively before relaxation. Here, we report the ultrafast spatiotemporal evolution of hot electrons in plasmonic resonators. Using femtosecond-resolution interferometric imaging, we show the unique periodic distributions of hot electrons due to standing plasmonic waves. In particular, this distribution can be flexibly tuned by the size, shape, and dimension of the resonator. We also demonstrate that the hot electron lifetimes are substantially prolonged at hot spots. This appealing effect is interpreted as a result of the locally concentrated energy density at the antinodes in standing hot electron waves. These results could be useful to control the distributions and lifetimes of hot electrons in plasmonic devices for targeted optoelectronic applications.

Plasmonic Cavity-Catalysis by Standing Hot Carrier Waves.

Manipulating active sites of catalysts is crucial but challenging in catalysis science and engineering. Beyond the design of the composition and structure of catalysts, the confined electromagnetic field in optical cavities has recently become a promising method for catalyzing chemical reactions via strong light-matter interactions. Another form of confined electromagnetic field, the charge density wave in plasmonic cavities, however, still needs to be explored for catalysis. Here, we present an unprecedented catalytic mode based on plasmonic cavities, called plasmonic cavity-catalysis. We achieve direct control of catalytic sites in plasmonic cavities through standing hot carrier waves. Periodic catalytic hotspots are formed because of localized energy and carrier distribution and can be well tuned by cavity geometry, charge density, and excitation angle. We also found that the catalytic activity of the cavity mode increases several orders of magnitude compared with conventional plasmonic catalysis. We ultimately demonstrate that the locally concentrated long-lived hot carriers in the standing wave mode underlie the formation of the catalytic hotspots. Plasmonic cavity-catalysis provides a new approach to manipulate the catalytic sites and rates and may expand the frontier of heterogeneous catalysis.

LRLoop: a method to predict feedback loops in cell-cell communication.

MOTIVATION: Intercellular communication (i.e. cell-cell communication) plays an essential role in multicellular organisms coordinating various biological processes. Previous studies discovered that feedback loops between two cell types are a widespread and vital signaling motif regulating development, regeneration and cancer progression. While many computational methods have been developed to predict cell-cell communication based on gene expression datasets, these methods often predict one-directional ligand-receptor interactions from sender to receiver cells and are not suitable to identify feedback loops. RESULTS: Here, we describe ligand-receptor loop (LRLoop), a new method for analyzing cell-cell communication based on bi-directional ligand-receptor interactions, where two pairs of ligand-receptor interactions are identified that are responsive to each other and thereby form a closed feedback loop. We first assessed LRLoop using bulk datasets and found our method significantly reduces the false positive rate seen with existing methods. Furthermore, we developed a new strategy to assess the performance of these methods in single-cell datasets. We used the between-tissue interactions as an indicator of potential false-positive prediction and found that LRLoop produced a lower fraction of between-tissue interactions than traditional methods. Finally, we applied LRLoop to the single-cell datasets obtained from retinal development. We discovered many new bi-directional ligand-receptor interactions among individual cell types that potentially control proliferation, neurogenesis and/or cell fate specification. AVAILABILITY AND IMPLEMENTATION: An R package is available at https://github.com/Pinlyu3/LRLoop. The source code can be found at figshare (https://doi.org/10.6084/m9.figshare.20126138.v1). The datasets can be found at figshare (https://doi.org/10.6084/m9.figshare.20126021.v1). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

URINARY METABOLOMICS OF CENTRAL SEROUS CHORIORETINOPATHY.

PURPOSE: To analyze the urinary metabolomic profile of central serous chorioretinopathy cases. METHODS: In a cross-sectional study, 80 participants with central serous chorioretinopathy were compared with 80 age-matched and sex-matched controls. Urinary metabolites were measured using Metabolon's Discovery HD4 platform. RESULTS: Of 1,031 metabolites total that were measured in urine samples, 53 were upregulated and 27 downregulated in central serous chorioretinopathy participants compared with controls. After exclusion of potentially confounding xenobiotics and bile compounds that could represent digestive processes, 14 metabolites were significantly higher and 12 metabolites were significantly lower in cases compared with controls. One upregulated metabolite (tetrahydrocortisol sulfate) is involved in the corticosteroid subpathway. The downregulated metabolites are unrelated to the identified corticosteroid subpathway. CONCLUSION: The upregulation of urinary tetrahydrocortisol sulfate in central serous chorioretinopathy cases provides a precise molecular basis to further study the role of corticosteroids in producing choroidal venous congestion.

Gate-Tunable Resonance State and Screening Effects for Proton-Like Atomic Charge in Graphene.

The ability to create a robust and well-defined artificial atomic charge in graphene and understand its carrier-dependent electronic properties represents an important goal toward the development of graphene-based quantum devices. Herein, we devise a new pathway toward the atomically precise embodiment of point charges into a graphene lattice by posterior (N) ion implantation into a back-gated graphene device. The N dopant behaves as an in-plane proton-like charge manifested by formation of the characteristic resonance state in the conduction band. Scanning tunneling spectroscopy measurements at varied charge carrier densities reveal a giant energetic renormalization of the resonance state up to 220 meV with respect to the Dirac point, accompanied by the observation of gate-tunable long-range screening effects close to individual N dopants. Joint density functional theory and tight-binding calculations with modified perturbation potential corroborate experimental findings and highlight the short-range character of N-induced perturbation.

Decrypting Material Performance by Wide-field Femtosecond Interferometric Imaging of Energy Carrier Evolution.

Energy carrier evolution is crucial for material performance. Ultrafast microscopy has been widely applied to visualize the spatiotemporal evolution of energy carriers. However, direct imaging of a small amount of energy carriers on the nanoscale remains difficult due to extremely weak transient signals. Here, we present a method for ultrasensitive and high-throughput imaging of energy carrier evolution in space and time. This method combines femtosecond pump-probe techniques with interferometric scattering microscopy (iSCAT), named Femto-iSCAT. The interferometric principle and unique spatially modulated contrast enhancement enable the exploration of new science. We address three important and challenging problems: transport of different energy carriers at various interfaces, heterogeneous hot-electron distribution and relaxation in single plasmonic resonators, and distinct structure-dependent edge-state dynamics of carriers and excitons in optoelectronic semiconductors. Femto-iSCAT holds great potential as a universal tool for ultrasensitive imaging of energy carrier evolution in space and time.

Printable two-dimensional superconducting monolayers.

Two-dimensional superconductor (2DSC) monolayers with non-centrosymmetry exhibit unconventional Ising pair superconductivity and an enhanced upper critical field beyond the Pauli paramagnetic limit, driving intense research interest. However, they are often susceptible to structural disorder and environmental oxidation, which destroy electronic coherence and provide technical challenges in the creation of artificial van der Waals heterostructures (vdWHs) for devices. Herein, we report a general and scalable synthesis of highly crystalline 2DSC monolayers via a mild electrochemical exfoliation method using flexible organic ammonium cations solvated with neutral solvent molecules as co-intercalants. Using NbSe2 as a model system, we achieved a high yield (>75%) of large-sized single-crystal monolayers up to 300 µm. The as-fabricated, twisted NbSe2 vdWHs demonstrate high stability, good interfacial properties and a critical current that is modulated by magnetic field when one flux quantum fits to an integer number of moiré cells. Additionally, formulated 2DSC inks can be exploited to fabricate wafer-scale 2D superconducting wire arrays and three-dimensional superconducting composites with desirable morphologies.

Electronic Self-Passivation of Single Vacancy in Black Phosphorus via Ionization.

We report that monoelemental black phosphorus presents a new electronic self-passivation scheme of single vacancy (SV). By means of low-temperature scanning tunneling microscopy and noncontact atomic force microscopy, we demonstrate that the local reconstruction and ionization of SV into negatively charged SV^{-} leads to the passivation of dangling bonds and, thus, the quenching of in-gap states, which can be achieved by mild thermal annealing or STM tip manipulation. SV exhibits a strong and symmetric Friedel oscillation (FO) pattern, while SV^{-} shows an asymmetric FO pattern with local perturbation amplitude reduced by one order of magnitude and a faster decay rate. The enhanced passivation by forming SV^{-} can be attributed to its weak dipolelike perturbation, consistent with density-functional theory numerical calculations. Therefore, self-passivated SV^{-} is electrically benign and acts as a much weaker scattering center, which may hold the key to further enhance the charge mobility of black phosphorus and its analogs.

Continuous Authentication against Collusion Attacks.

As mobile devices become more and more popular, users gain many conveniences. It has also made smartphone makers install new software and prebuilt hardware on their products, including many kinds of sensors. With improved storage and computing power, users also become accustomed to storing and interacting with personally sensitive information. Due to convenience and efficiency, mobile devices use gait authentication widely. In recent years, protecting the information security of mobile devices has become increasingly important. It has become a hot research area because smartphones are vulnerable to theft or unauthorized access. This paper proposes a novel attack model called a collusion attack. Firstly, we study the imitation attack in the general state and its results and propose and verify the feasibility of our attack. We propose a collusion attack model and train participants with quantified action specifications. The results demonstrate that our attack increases the attacker's false match rate only using an acceleration sensor in some systems sensor. Furthermore, we propose a multi-cycle defense model based on acceleration direction changes to improve the robustness of smartphone-based gait authentication methods against such attacks. Experimental results show that our defense model can significantly reduce the attacker's success rate.

New Advances in Using Virus-like Particles and Related Technologies for Eukaryotic Genome Editing Delivery.

The designer nucleases, including Zinc Finger Nuclease (ZFN), Transcription Activator-Like Effector Nuclease (TALEN), and Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated (CRISPR/Cas), have been widely used for mechanistic studies, animal model generation, and gene therapy development. Clinical trials using designer nucleases to treat genetic diseases or cancers are showing promising results. Despite rapid progress, potential off-targets and host immune responses are challenges to be addressed for in vivo uses, especially in clinical applications. Short-term expression of the designer nucleases is necessary to reduce both risks. Currently, delivery methods enabling transient expression of designer nucleases are being pursued. Among these, virus-like particles as delivery vehicles for short-term designer nuclease expression have received much attention. This review will summarize recent developments in using virus-like particles (VLPs) for safe delivery of gene editing effectors to complement our last review on the same topic. First, we introduce some background information on how VLPs can be used for safe and efficient CRISPR/Cas9 delivery. Then, we summarize recently developed virus-like particles as genome editing vehicles. Finally, we discuss applications and future directions.

Delivering Cas9/sgRNA ribonucleoprotein (RNP) by lentiviral capsid-based bionanoparticles for efficient 'hit-and-run' genome editing.

Transient expression of the CRISPR/Cas9 machinery will not only reduce risks of mutagenesis from off-target activities, but also decrease possible immune response to Cas9 protein. Building on our recent developing of a system able to package up to 100 copies of Cas9 mRNA in each lentivirus-like particle (LVLP) via the specific interaction between aptamer and aptamer-binding proteins (ABP), here we develop a lentiviral capsid-based bionanoparticle system, which allows efficient packaging of Cas9/sgRNA ribonucleoprotein (RNP). We show that replacing the Tetraloop of sgRNA scaffold with a com aptamer preserves the functions of the guide RNA, and the com-modified sgRNA can package Cas9/sgRNA RNP into lentivirus-like particles via the specific interactions between ABP and aptamer, and sgRNA and Cas9 protein. These RNP bionanoparticles generated Indels on different targets in different cells with efficiencies similar to or better than our recently described Cas9 mRNA LVLPs. The new system showed fast action and reduced off-target rates, and makes it more convenient and efficient in delivering Cas9 RNPs for transient Cas9 expression and efficient genome editing.

Delivering SaCas9 mRNA by lentivirus-like bionanoparticles for transient expression and efficient genome editing.

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system discovered using bacteria has been repurposed for genome editing in human cells. Transient expression of the editor proteins (e.g. Cas9 protein) is desirable to reduce the risk of mutagenesis from off-target activity. Using the specific interaction between bacteriophage RNA-binding proteins and their RNA aptamers, we developed a system able to package up to 100 copies of Staphylococcus aureus Cas9 (SaCas9) mRNA in each lentivirus-like bionanoparticle (LVLP). The SaCas9 LVLPs mediated transient SaCas9 expression and achieved highly efficient genome editing in the presence of guide RNA. Lower off-target rates occurred in cells transduced with LVLPs containing SaCas9 mRNA, compared with cells transduced with adeno-associated virus or lentivirus expressing SaCas9. Our LVLP system may be useful for efficiently delivering Cas9 mRNA to cell lines and primary cells for in vitro and in vivo gene editing applications.

CRISPR/Cas9 increases mitotic gene conversion in human cells.

Gene conversion is a process of transferring genetic material from one homologous sequence to another. Most reported gene conversions are meiotic although mitotic gene conversion is also described. When using CRISPR/Cas9 to target the human hemoglobin subunit beta (HBB) gene, hemoglobin subunit delta (HBD) gene footprints were observed in HBB gene. However, it is unclear whether these were the results of gene conversion or PCR-mediated sequence shuffling between highly homologous sequences. Here we provide evidence that the HBD footprints in HBB were indeed results of gene conversion. We demonstrated that the CRISPR/Cas9 facilitated unidirectional sequence transfer from the homologous gene without double-strand breaks (DSB) to the one with DSBs, and showed that the rates of HBD footprint in HBB were positively correlated to the HBB insertion and deletion rates. We further showed that when targeting HBD gene, HBB footprints could also be observed in HBD gene. The mitotic gene conversion was observed not only in immortalized HEK293T cells, but also in human primary cells. Our work reveals mitotic gene conversion as an often overlooked effect of CRISPR/Cas9-mediated genome editing.

Real-Space Imaging of a Single-Molecule Monoradical Reaction.

Organic radicals consisting of light elements exhibit a low spin-orbit coupling and weak hyperfine interactions with a long spin coherence length, which are crucial for future applications in molecular spintronics. However, the synthesis and characterization of these organic radicals have been a formidable challenge due to their chemical instability arising from unpaired electrons. Here, we report a direct imaging of the surface chemical transformation of an organic monoradical synthesized via the monodehydrogenation of a chemically designed precursor. Bond-resolved scanning tunneling microscopy unambiguously resolves various products formed through a complex structural dissociation and rearrangement of organic monoradicals. Density functional theory calculations reveal detailed reaction pathways from the monoradical to different cyclized products. Our study provides unprecedented insights into complex surface reaction mechanisms of organic radical reactions at the single molecule level, which may guide the design of stable organic radicals for future quantum technology applications.