MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain.

In vitro studies indicate the neurodevelopmental disorder gene myelin transcription factor 1-like (MYT1L) suppresses non-neuronal lineage genes during fibroblast-to-neuron direct differentiation. However, MYT1L's molecular and cellular functions in the adult mammalian brain have not been fully characterized. Here, we found that MYT1L loss leads to up-regulated deep layer (DL) gene expression, corresponding to an increased ratio of DL/UL neurons in the adult mouse cortex. To define potential mechanisms, we conducted Cleavage Under Targets & Release Using Nuclease (CUT&RUN) to map MYT1L binding targets and epigenetic changes following MYT1L loss in mouse developing cortex and adult prefrontal cortex (PFC). We found MYT1L mainly binds to open chromatin, but with different transcription factor co-occupancies between promoters and enhancers. Likewise, multiomic data set integration revealed that, at promoters, MYT1L loss does not change chromatin accessibility but increases H3K4me3 and H3K27ac, activating both a subset of earlier neuronal development genes as well as Bcl11b, a key regulator for DL neuron development. Meanwhile, we discovered that MYT1L normally represses the activity of neurogenic enhancers associated with neuronal migration and neuronal projection development by closing chromatin structures and promoting removal of active histone marks. Further, we showed that MYT1L interacts with HDAC2 and transcriptional repressor SIN3B in vivo, providing potential mechanisms underlying repressive effects on histone acetylation and gene expression. Overall, our findings provide a comprehensive map of MYT1L binding in vivo and mechanistic insights into how MYT1L loss leads to aberrant activation of earlier neuronal development programs in the adult mouse brain.

ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers.

Accurate understanding of the biological functions of enzymes is vital for various tasks in both pathologies and industrial biotechnology. However, the existing methods are usually not fast enough and lack explanations on the prediction results, which severely limits their real-world applications. Following our previous work, DEEPre, we propose a new interpretable and fast version (ifDEEPre) by designing novel self-guided attention and incorporating biological knowledge learned via large protein language models to accurately predict the commission numbers of enzymes and confirm their functions. Novel self-guided attention is designed to optimize the unique contributions of representations, automatically detecting key protein motifs to provide meaningful interpretations. Representations learned from raw protein sequences are strictly screened to improve the running speed of the framework, 50 times faster than DEEPre while requiring 12.89 times smaller storage space. Large language modules are incorporated to learn physical properties from hundreds of millions of proteins, extending biological knowledge of the whole network. Extensive experiments indicate that ifDEEPre outperforms all the current methods, achieving more than 14.22% larger F1-score on the NEW dataset. Furthermore, the trained ifDEEPre models accurately capture multi-level protein biological patterns and infer evolutionary trends of enzymes by taking only raw sequences without label information. Meanwhile, ifDEEPre predicts the evolutionary relationships between different yeast sub-species, which are highly consistent with the ground truth. Case studies indicate that ifDEEPre can detect key amino acid motifs, which have important implications for designing novel enzymes. A web server running ifDEEPre is available at https://proj.cse.cuhk.edu.hk/aihlab/ifdeepre/ to provide convenient services to the public. Meanwhile, ifDEEPre is freely available on GitHub at https://github.com/ml4bio/ifDEEPre/.

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis.

We present a novel self-supervised Contrastive LEArning framework for single-cell ribonucleic acid (RNA)-sequencing (CLEAR) data representation and the downstream analysis. Compared with current methods, CLEAR overcomes the heterogeneity of the experimental data with a specifically designed representation learning task and thus can handle batch effects and dropout events simultaneously. It achieves superior performance on a broad range of fundamental tasks, including clustering, visualization, dropout correction, batch effect removal, and pseudo-time inference. The proposed method successfully identifies and illustrates inflammatory-related mechanisms in a COVID-19 disease study with 43 695 single cells from peripheral blood mononuclear cells.

AcrNET: predicting anti-CRISPR with deep learning.

MOTIVATION: As an important group of proteins discovered in phages, anti-CRISPR inhibits the activity of the immune system of bacteria (i.e. CRISPR-Cas), offering promise for gene editing and phage therapy. However, the prediction and discovery of anti-CRISPR are challenging due to their high variability and fast evolution. Existing biological studies rely on known CRISPR and anti-CRISPR pairs, which may not be practical considering the huge number. Computational methods struggle with prediction performance. To address these issues, we propose a novel deep neural network for anti-CRISPR analysis (AcrNET), which achieves significant performance. RESULTS: On both the cross-fold and cross-dataset validation, our method outperforms the state-of-the-art methods. Notably, AcrNET improves the prediction performance by at least 15% regarding the F1 score for the cross-dataset test problem comparing with state-of-art Deep Learning method. Moreover, AcrNET is the first computational method to predict the detailed anti-CRISPR classes, which may help illustrate the anti-CRISPR mechanism. Taking advantage of a Transformer protein language model ESM-1b, which was pre-trained on 250 million protein sequences, AcrNET overcomes the data scarcity problem. Extensive experiments and analysis suggest that the Transformer model feature, evolutionary feature, and local structure feature complement each other, which indicates the critical properties of anti-CRISPR proteins. AlphaFold prediction, further motif analysis, and docking experiments further demonstrate that AcrNET can capture the evolutionarily conserved pattern and the interaction between anti-CRISPR and the target implicitly. AVAILABILITY AND IMPLEMENTATION: Web server: https://proj.cse.cuhk.edu.hk/aihlab/AcrNET/. Training code and pre-trained model are available at.

Invertible all-optical logic gate on chip.

We demonstrate an invertible all-optical gate on chip, with the roles of control and signal switchable by slightly adjusting their relative arrival time at the gate. It is based on the quantum Zeno blockade (QZB) driven by sum-frequency generation (SFG) in a periodically poled lithium niobate microring resonator. For two nearly identical nanosecond pulses, the later arriving pulse is modulated by the earlier arriving one, resulting in 2.4 and 3.9 power extinction between the two, respectively, when their peak powers are 1 mW and 2 mW, respectively. Our results, while to be improved and enriched, herald a new, to the best of our knowledge, paradigm of logical gates and circuits for exotic applications.

Broadband frequency comb generation through cascaded quadratic nonlinearity in thin-film lithium niobate microresonators.

Broadband frequency comb generation through cascaded quadratic nonlinearity remains experimentally untapped in free-space cavities with bulk χ(2) materials mainly due to the high threshold power and restricted ability of dispersion engineering. Thin-film lithium niobate (LN) is a good platform for nonlinear optics due to the tight mode confinement in a nano-dimensional waveguide, the ease of dispersion engineering, large quadratic nonlinearities, and flexible phase matching via periodic poling. Here we demonstrate broadband frequency comb generation through dispersion engineering in a thin-film LN microresonator. Bandwidths of 150 nm (80 nm) and 25 nm (12 nm) for center wavelengths at 1560 and 780 nm are achieved, respectively, in a cavity-enhanced second-harmonic generation (doubly resonant optical parametric oscillator). Our demonstration paves the way for pure quadratic soliton generation, which is a great complement to dissipative Kerr soliton frequency combs for extended interesting nonlinear applications.

Evaluating Losses from Water Scarcity and Benefits of Water Conservation Measures to Intercity Supply Chains in China.

The severe water scarcity in China poses significant economic risks to its agriculture, energy, and manufacturing sectors, which can have a cascading effect through the supply chains. Current research has assessed water scarcity losses for global countries and Chinese provinces by using the water scarcity risk (WSR) method. However, this method involves subjective functions and parameter settings, and it fails to capture the adaptive behaviors of economies to water scarcity, compromising the reliability of quantified water scarcity loss. There is a pressing need for a new method to assess losses related to water scarcity. Here, we develop an agent-based complex network model to estimate the inter-regional and intersectoral impacts of water scarcity on both cities and basins. Subsequently, we evaluate the supply chain-wide economic benefits of four different water conservation measures as stipulated by the 14th Five-Year Plan for the Construction of a Water-Saving Society. These measures include increasing the utilization rate of recycled water in water-scarce cities, reducing the national water consumption per industrial value-added, and implementing agricultural and residential water conservation measures. Results show that direct losses constitute only 9% of the total losses from water scarcity. Approximately 37% of the losses can be attributed to interregional impacts. Among the water-scarce cities, Qingdao, Lanzhou, Jinan, and Zhengzhou pose a significant threat to China's supply chains. Agricultural water conservation yields the highest amount of water savings and economic benefits, while residential water conservation provides the highest economic benefit per unit of water saved. The results provide insights into managing water scarcity, promoting cross-regional cooperation, and mitigating economic impacts.

Significantly Enhanced Robustness of K Isotope Analysis by Collision Cell MC-ICP-MS and Its Application to the Returned Lunar Samples by China's Chang'e-5 Project.

Stable K isotope ratios, an emerging research tool for a wide range of problems, can be measured precisely with high sensitivity by using collision cell multicollector ICP mass spectrometers (CC-MC-ICP-MS). However, it has been shown that the accuracy of K isotope analysis by CC-MC-ICP-MS could be compromised severely by trace-level Ca contaminants, although the cause of such an effect remains poorly understood. Here, we report that the influence of Ca on K isotope analysis by CC-MC-ICP-MS can be dramatically reduced if D2 rather than H2 (the default gas) is used as the reaction gas that goes into the collision cell. This indicates the generation of positively charged calcium-hydride molecules in the collision cell. Usage of D2 as reaction gas circumvents the Ca-induced inaccuracy issues during K isotope analysis because 40CaD+ does not interfere with 41K+ as 40CaH+ does; as such, the robustness of K isotope analysis by CC-MC-ICP-MS is significantly enhanced. This improved method is verified by K isotope analysis of seven geostandards, and applied to China's Chang'e-5 lunar return samples at submicrogram K consumption, revealing significant K isotope variability within a 17 mg lunar basalt fragment.

Femtosecond-laser-based full-field three-dimensional imaging with phase compensation.

Coherence scanning interferometer (CSI) enables 3D imaging with nanoscale precision. However, the efficiency of such a system is limited because of the restriction imposed by the acquisition system. Herein, we propose a phase compensation method that reduces the interferometric fringe period of femtosecond-laser-based CSI, resulting in larger sampling intervals. We realize this method by synchronizing the heterodyne frequency with the repetition frequency of the femtosecond laser. The experimental results show that our method can keep the root-mean-square axial error down to 2 nm at a high scanning speed of 6.44 µm per frame, which enables fast nanoscale profilometry over a wide area.

Photo- or Electrochemical Cyclization of Dienes with Diselenides to Access Seleno-Benzo[b]azepines.

A cascade selenylation/cyclization of dienes with diselenides has been realized under visible-light irradiation or electrolysis conditions. Employing O2 or electricity as a "green" oxidant, this protocol provides a green and efficient method for an array of biologically important seleno-benzo[b]azepine derivatives in moderate to good yields. The direct sunlight irradiation and gram-scale reaction render the approach practical and attractive.

High Selectivity Cofactor NADH Regeneration Organic Iridium Complexes Used for High-Efficiency Chem-Enzyme Cascade Catalytic Hydrogen Transfer.

Our research demonstrated that novel pentamethylcyclopentadienyl (Cp*) iridium pyridine sulfonamide complex PySO2NPh-Ir (7) could highly specifically catalyze nicotinamide adenine dinucleotide (NAD+) into the corresponding reducing cofactor NADH in cell growth media containing various biomolecules. The structures and catalytic mechanism of 7 were studied by single-crystal X-ray, NMR, electrochemical, and kinetic methods, and the formation of iridium hydride species Ir-H was confirmed to be the plausible hydride-transfer intermediate of 7. Moreover, benefiting from its high hydrogen-transfer activity and selectivity for NADH regeneration, 7 was used as an optimal metal catalyst to establish a chem-enzyme cascade catalytic hydrogen-transfer system, which realized the high-efficiency preparation of l-glutamic acid by combining with l-glutamate dehydrogenase (GLDH).

A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues.

Transcription factors (TFs) enact precise regulation of gene expression through site-specific, genome-wide binding. Common methods for TF-occupancy profiling, such as chromatin immunoprecipitation, are limited by requirement of TF-specific antibodies and provide only end-point snapshots of TF binding. Alternatively, TF-tagging techniques, in which a TF is fused to a DNA-modifying enzyme that marks TF-binding events across the genome as they occur, do not require TF-specific antibodies and offer the potential for unique applications, such as recording of TF occupancy over time and cell type specificity through conditional expression of the TF-enzyme fusion. Here, we create a viral toolkit for one such method, calling cards, and demonstrate that these reagents can be delivered to the live mouse brain and used to report TF occupancy. Further, we establish a Cre-dependent calling cards system and, in proof-of-principle experiments, show utility in defining cell type-specific TF profiles and recording and integrating TF-binding events across time. This versatile approach will enable unique studies of TF-mediated gene regulation in live animal models.

Compression-coding-based surface measurement using a digital micromirror device and heterodyne interferometry of an optical frequency comb.

We propose a compression-coding-based surface measurement method that combines single-pixel imaging and heterodyne interference using an optical frequency comb. The real and imaginary parts of the heterodyne interference signals are used to obtain the depth information rapidly. By optimizing the ordering of the Hadamard measurement basis, we reconstruct a three-step sample with heights of approximately 10, 20, and 30 µm without an iterative operation in 6 ms, with a precision of 5 nm. Compared with the uncompressed measurement, the sampling times reduced to 20%, and the measurement time reduced by five times without measurement accuracy loss. The proposed method is effective for rapid measurements, particularly for objects with a simple surface topography.

Multi-color method for the self-correction of the air refractive index.

We propose a multi-color method for the self-correction of the air refractive index based on the dispersive interferometry of an optical frequency comb. This method can be applied to correct the air refractive index for long-distance measurements in moist air. Optical lengths of multiple wavelengths were obtained simultaneously by the dispersive interferometry of an optical frequency comb. Interferometric measurement results and calculations from the empirical equation of air refractive indices were similar, with a standard deviation of 2.0×10-9 throughout the 2 h continuous measurement period. By applying the multi-color method, correction of the air refractive index with an uncertainty of 3.5×10-7 was achieved.

Efficient electro-optical modulation on thin-film lithium niobate.

Thin-film lithium niobate has emerged as an excellent, multifaceted platform for integrated photonics and opto-electronics, in both classical and quantum domains. We introduce a novel, to the best of our knowledge, dual-capacitor electrode layout for an efficient interface between electrical and optical signals on this platform. It significantly enhances the electro-optical modulation efficiency to an exceptional voltage-length product of 0.64V⋅cm, thereby lowering the required electric power by many times. This technique can boost the performance of growing applications at the interface of integrated electronics and optics, such as microwave photonics, frequency comb generation, and telecommunication transmission.

Efficient electro-optical modulation on thin-film lithium niobate: erratum.

In this erratum, we correct the corresponding results of our Letter [Opt. Lett.46, 1884 (2021)OPLEDP0146-959210.1364/OL.419597] due to the wrong impedance setting of the arbitrary waveform generator (AWG). The Letter still represents the significant advance despite the change of results.

Circ_0091581 Promotes the Progression of Hepatocellular Carcinoma Through Targeting miR-591/FOSL2 Axis.

BACKGROUND: Circular RNAs (circRNAs) have shown crucial regulatory roles in cancer biology. We aimed to uncover the role and underlying mechanism of circ_0091581 in hepatocellular carcinoma (HCC) progression. METHODS: The abundance of circ_0091581, microRNA-591 (miR-591) and FOS like 2, AP-1 transcription factor subunit (FOSL2) was measured by quantitative real-time polymerase chain reaction. Cell viability, colony formation ability, and invasion ability were assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, colony formation assay, and transwell invasion assay. The migration ability was analyzed by transwell migration assay and wound healing assay. Flow cytometry was used to evaluate the cell cycle and apoptosis of HCC cells. The interaction between miR-591 and circ_0091581 or FOSL2 was predicted by Circular RNA Interactome database or TargetScan database and confirmed by dual-luciferase reporter assay and RNA immune co-precipitation assay. FOSL2 protein expression was measured by Western blot assay. Xenograft tumor assay was conducted to analyze the role of circ_0091581 in HCC tumor growth in vivo. RESULTS: Circ_0091581 was highly expressed in HCC tissue samples and cell lines in contrast to that in adjacent normal tissue samples and THLE-2 cell line. Circ_0091581 accelerated the viability, colony formation, metastasis, and cell cycle, while it impeded the apoptosis of HCC cells. MiR-591 bound to circ_0091581, and circ_0091581 knockdown-mediated effects in HCC cells were largely overturned by miR-591 silencing. FOSL2 was a target of miR-591, and FOSL2 overexpression largely reversed miR-591 accumulation-induced influences in HCC cells. FOSL2 protein expression was down-regulated by circ_0091581 silencing, and the addition of miR-591 inhibitor partly recovered the expression of FOSL2 in HCC cells. Circ_0091581 interference notably suppressed HCC tumor growth in vivo. CONCLUSION: Circ_0091581 acted as an oncogene to enhance the viability, colony formation, metastasis and cell cycle and inhibit the apoptosis of HCC cells through targeting miR-591/FOSL2 axis.

An enhanced photoelectrochemical biosensor for colitoxin DNA based on HKUST-1/TiO2 and derived HKUST-CuO/TiO2 heterogeneous composites.

HKUST-1 MOFs and its derivative HKUST-CuO were coupled with TiO2 nanoparticles to form the heterogeneous composites of HKUST-1/TiO2 and HKUST-CuO/TiO2 based on their well-suitable bandgap energies (Eg). Compared with mono-component HKUST-1 or HKUST-CuO, the prepared composites displayed photoelectrochemical (PEC) response due to the synergistic effect from their heterogeneous structure. Higher photocurrent response was obtained on HKUST-CuO/TiO2-modified ITO electrode (HKUST-CuO/TiO2/ITO), which could be attributed to the hollow structure with a thin shell of HKUST-CuO greatly enhancing visible spectra harvesting. The CuO component in HKUST-CuO not only could accelerate electron transfer on the heterojunction interface but also effectively separate the photo-generated charge carriers (e-1/h+). Based on the excellent PEC performance of prepared photoactive composite material, under visible-light excitation (λ ≥ 420 nm) and with a working potential of 0 V (vs. Ag/AgCl), the S1 (probe DNA)/HKUST-CuO/TiO2/ITO PEC platform was successfully fabricated for colitoxin DNA detection without using ascorbic acid (AA) as an electron donor. Compared with the analysis results on S1/HKUST-1/TiO2/ITO electrode, S1/HKUST-CuO/TiO2/ITO displayed a wider linear response range from 1.0 × 10-6 to 4.0 × 10-1 nM with a lower detection limit of 3.73 × 10-7 nM (S/N = 3), the linear regression equation was ΔI (10-6 A) =0.5549-0.1858 log (CS2/M), which confirmed the HKUST-CuO could improve sensitivity because of its prominent PEC property. The relative standard deviation (RSD) of the PEC sensor for target DNA detection of 2.0 × 10-4 nM was 7.4%. The proposed DNA biosensor also possessed good specificity and stability. Hence, this reported work was a promising strategy for molecular diagnosis in the bio-analysis field. (A) Schematic illustration of the preparation process of the proposed PEC biosensors for colitoxin DNA detection. (B) The preparation process of HKUST-1 and HKUST-CuO.

Efficient and highly tunable second-harmonic generation in Z-cut periodically poled lithium niobate nanowaveguides.

Thin-film lithium-niobate-on-insulator (LNOI) has emerged as a superior integrated-photonics platform for linear, nonlinear, and electro-optics. Here we combine quasi-phase-matching, dispersion engineering, and tight mode confinement to realize nonlinear parametric processes with both high efficiency and wide wavelength tunability. On a millimeter-long, Z-cut LNOI waveguide, we demonstrate efficient (1900±500%W-1cm-2) and highly tunable (-1.71nm/K) second-harmonic generation from 1530 to 1583 nm by type-0 quasi-phase-matching. Our technique is applicable to optical harmonic generation, quantum light sources, frequency conversion, and many other photonic information processes across visible to mid-IR spectral bands.

Ultrabright Quantum Photon Sources on Chip.

Quantum photon sources of high rate, brightness, and purity are increasingly desirable as quantum information systems are quickly scaled up and applied to many fields. Using a periodically poled lithium niobate microresonator on chip, we demonstrate photon-pair generation at high rates of 8.5 and 36.3 MHz using only 3.4 and 13.4 µW pump power, respectively, marking orders of magnitude improvement over the state of the art, across all material platforms. These results constitute the first direct measurement of the device's giant single photon nonlinearity. The measured coincidence to accidental ratio is well above 100 at those high rates and reaches 14682±4427 at a lower pump power. The same chip enables heralded single-photon generation at tens of megahertz rates, each with low autocorrelation g_{H}^{(2)}(0)=0.008 and 0.097 for the microwatt pumps, which marks a new milestone. Such distinct performance, facilitated by the chip device's noiseless and giant optical nonlinearity, will contribute to the forthcoming pervasive adoption of quantum optical information technologies.