Syndromic immune disorder caused by a viable hypomorphic allele of spliceosome component Snrnp40.

We report a new immunodeficiency disorder in mice caused by a viable hypomorphic mutation of Snrnp40, an essential gene encoding a subunit of the U5 small nuclear ribonucleoprotein (snRNP) complex of the spliceosome. Snrnp40 is ubiquitous but strongly expressed in lymphoid tissue. Homozygous mutant mice showed hypersusceptibility to infection by murine cytomegalovirus and multiple defects of lymphoid development, stability and function. Cell-intrinsic defects of hematopoietic stem cell differentiation also affected homozygous mutants. SNRNP40 deficiency in primary hematopoietic stem cells or T cells or the EL4 cell line increased the frequency of splicing errors, mostly intron retention, in several hundred messenger RNAs. Altered expression of proteins associated with immune cell function was also observed in Snrnp40-mutant cells. The immunological consequences of SNRNP40 deficiency presumably result from cumulative, moderate effects on processing of many different mRNA molecules and secondary reductions in the expression of critical immune proteins, yielding a syndromic immune disorder.

CDK7 regulates organ size and tumor growth by safeguarding the Hippo pathway effector Yki/Yap/Taz in the nucleus.

Hippo signaling controls organ size and tumor progression through a conserved pathway leading to nuclear translocation of the transcriptional effector Yki/Yap/Taz. Most of our understanding of Hippo signaling pertains to its cytoplasmic regulation, but how the pathway is controlled in the nucleus remains poorly understood. Here we uncover an evolutionarily conserved mechanism by which CDK7 promotes Yki/Yap/Taz stabilization in the nucleus to sustain Hippo pathway outputs. We found that a modular E3 ubiquitin ligase complex CRL4DCAF12 binds and targets Yki/Yap/Taz for ubiquitination and degradation, whereas CDK7 phosphorylates Yki/Yap/Taz at S169/S128/S90 to inhibit CRL4DCAF12 recruitment, leading to Yki/Yap/Taz stabilization. As a consequence, inactivation of CDK7 reduced organ size and inhibited tumor growth, which could be reversed by restoring Yki/Yap activity. Our study identifies an unanticipated layer of Hippo pathway regulation, defines a novel mechanism by which CDK7 regulates tissue growth, and implies CDK7 as a drug target for Yap/Taz-driven cancer.

AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations.

Transcription factors (TFs) are proteins that interact with specific DNA sequences to regulate gene expression and play crucial roles in all kinds of biological processes. To keep up with new data and provide a more comprehensive resource for TF research, we updated the Animal Transcription Factor Database (AnimalTFDB) to version 4.0 (http://bioinfo.life.hust.edu.cn/AnimalTFDB4/) with up-to-date data and functions. We refined the TF family rules and prediction pipeline to predict TFs in genome-wide protein sequences from Ensembl. As a result, we predicted 274 633 TF genes and 150 726 transcription cofactor genes in AnimalTFDB 4.0 in 183 animal genomes, which are 86 more species than AnimalTFDB 3.0. Besides double data volume, we also added the following new annotations and functions to the database: (i) variations (including mutations) on TF genes in various human cancers and other diseases; (ii) predicted post-translational modification sites (including phosphorylation, acetylation, methylation and ubiquitination sites) on TFs in 8 species; (iii) TF regulation in autophagy; (iv) comprehensive TF expression annotation for 38 species; (v) exact and batch search functions allow users to search AnimalTFDB flexibly. AnimalTFDB 4.0 is a useful resource for studying TF and transcription regulation, which contains comprehensive annotation and classification of TFs and transcription cofactors.

1,25(OH)2 D3 inhibits Lewis lung cancer cell migration via NHE1-sensitive metabolic reprograming.

High prevalence and metastasis rates are characteristics of lung cancer. Glycolysis provides energy for the development and metastasis of cancer cells. The 1,25-dihydroxy vitamin D3 (1,25(OH)2 D3 ) has been linked to reducing cancer risk and regulates various physiological functions. We hypothesized that 1,25(OH)2 D3 could be associated with the expression and activity of Na+ /H+ exchanger isoform 1 (NHE1) of Lewis lung cancer cells, thus regulating glycolysis as well as migration by actin reorganization. Followed by online public data analysis, Vitamin D3 receptor, the receptor of 1,25(OH)2 D3 has been proved to be abundant in lung cancers. We demonstrated that 1,25(OH)2 D3 treatment suppressed transcript levels, protein levels, and activity of NHE1 in LLC cells. Furthermore, 1,25(OH)2 D3 treatment resets the metabolic balance between glycolysis and OXPHOS, mainly including reducing glycolytic enzymes expression and lactate production. In vivo experiments showed the inhibition effects on tumor growth as well. Therefore, we concluded that 1,25(OH)2 D3 could amend the NHE1 function, which leads to metabolic reprogramming and cytoskeleton reconstruction, finally inhibits the cell migration.

Aluminum-based plasmonic metasurface for computational spectrometry with full coverage of visible light.

Reconstructive spectrometers/spectral cameras have immense potential for portable applications in various fields, including environmental monitoring, biomedical research and diagnostics, and agriculture and food safety. However, the performance of these spectrometers/spectral cameras is severely limited by the operational bandwidth, spectral diversity, and angle sensitivity of the spectral modulation devices. In this work, we propose a compact spectrometer based on plasmonic metasurfaces that operate across the entire visible wavelength range, covering wavelengths from 400 to 750 nm. We experimentally demonstrate the effective spectral reconstruction achieved by the designed metasurface spectrometer, exhibiting angle tolerance to the incident light within the range of ± 12°. Our results highlight the potential for constructing broadband, large field-of-view hyperspectral cameras.

Glucocorticoids promote joint microenvironment alteration of GABBR1 expression associated with mitigating rheumatoid arthritis.

GABBR1 receptors have been implicated in the progression of rheumatoid arthritis (RA), and p38 MAP kinase (MAPK) was shown to be downregulated by GABA and result in unchecked production of pro-inflammatory cytokine. GABBR1 is a member of GABA receptors, and it is known to be upregulated and plays a vital role in RA. Glucocorticoids are efficient therapeutics in rheumatoid arthritis (RA) and are known to regulate GABA actions; therefore, we intended to investigate the potential of glucocorticoids in RA concerning the potential pathway GABBR1/MAPK. Joint specimens were obtained from collagen-induced arthritis mouse model. A double-blind semi-quantitative analysis of vascularity, cell infiltration, as well as lining thickness by help of a 4-point scale setting was used to assess joint inflammation. Expression of GABBR1 and p38 was evaluated immunohistochemically. In vitro peripheral blood (PB), synovial fluid (SF), and mononuclear cells (MCs) were acquired from RA mice. Western blotting was used for detecting expression of GABBR1 and p38 proteins. The presence of high levels of GABBR1 and p38 was prevalent in RA joints relative to healthy joints and related to the inflammation level. Glucocorticoid treatment alters GABBR1 along with p38 protein expression in joints while reducing joint inflammation. Ex vivo and in vitro assays revealed glucocorticoids have a direct impact on p38, such as the decreased GABBR1 expression level after dexamethasone incubation with SFMC. GABBR1 together with p38 expression in RA joints depends on local inflammation and can be targeted by glucocorticoids.

Review on magnetic adsorbents for removal of elemental mercury from coal combustion flue gas.

Under the influence of human activities, atmospheric mercury (Hg) concentrations have increased by 450% compared with natural levels. In the context of the Minamata Convention on Mercury, which came into effect in August 2017, it is imperative to strengthen Hg emission controls. Existing Air Pollution Control Devices (APCDs) combined with collaborative control technology can effectively remove Hg2+ and Hgp; however, Hg0 removal is substandard. Compared with the catalytic oxidation method, Hg0 removal through adsorbent injection carries the risk of secondary release and is uneconomical. Magnetic adsorbents exhibit excellent recycling and Hg0 recovery performance and have recently attracted the attention of researchers. This review summarizes the existing magnetic materials for Hg0 adsorption and discusses the removal performances and mechanisms of iron, carbon, mineral-based, and magnetosphere materials. The effects of temperature and different flue gas components, including O2, NO, SO2, H2O, and HCl, on the adsorption performance of Hg0 are also summarized. Finally, different regeneration methods are discussed in detail. Although the research and development of magnetic adsorbents has progressed, significant challenges remain regarding their application. This review provides theoretical guidance for the improvement of existing and development of new magnetic adsorbents.

Sulfatides are endogenous ligands for the TLR4-MD-2 complex.

Many endogenous molecules, mostly proteins, purportedly activate the Toll-like receptor 4 (TLR4)-myeloid differentiation factor-2 (MD-2) complex, the innate immune receptor for lipopolysaccharide (LPS) derived from gram-negative bacteria. However, there is no structural evidence supporting direct TLR4-MD-2 activation by endogenous ligands. Sulfatides (3-O-sulfogalactosylceramides) are natural, abundant sulfated glycolipids that have variously been shown to initiate or suppress inflammatory responses. We show here that short fatty acid (FA) chain sulfatides directly activate mouse TLR4-MD-2 independent of CD14, trigger MyD88- and TRIF-dependent signaling, and stimulate tumor necrosis factor α (TNFα) and type I interferon (IFN) production in mouse macrophages. In contrast to the agonist activity toward the mouse receptor, the tested sulfatides antagonize TLR4-MD-2 activation by LPS in human macrophage-like cells. The agonistic and antagonistic activities of sulfatides require the presence of the sulfate group and are inversely related to the FA chain length. The crystal structure of mouse TLR4-MD-2 in complex with C16-sulfatide revealed that three C16-sulfatide molecules bound to the MD-2 hydrophobic pocket and induced an active dimer conformation of the receptor complex similar to that induced by LPS or lipid A. The three C16-sulfatide molecules partially mimicked the detailed interactions of lipid A to achieve receptor activation. Our results suggest that sulfatides may mediate sterile inflammation or suppress LPS-stimulated inflammation, and that additional endogenous negatively charged lipids with up to six lipid chains of limited length might also bind to TLR4-MD-2 and activate or inhibit this complex.

Thousands of induced germline mutations affecting immune cells identified by automated meiotic mapping coupled with machine learning.

Forward genetic studies use meiotic mapping to adduce evidence that a particular mutation, normally induced by a germline mutagen, is causative of a particular phenotype. Particularly in small pedigrees, cosegregation of multiple mutations, occasional unawareness of mutations, and paucity of homozygotes may lead to erroneous declarations of cause and effect. We sought to improve the identification of mutations causing immune phenotypes in mice by creating Candidate Explorer (CE), a machine-learning software program that integrates 67 features of genetic mapping data into a single numeric score, mathematically convertible to the probability of verification of any putative mutation-phenotype association. At this time, CE has evaluated putative mutation-phenotype associations arising from screening damaging mutations in ∼55% of mouse genes for effects on flow cytometry measurements of immune cells in the blood. CE has therefore identified more than half of genes within which mutations can be causative of flow cytometric phenovariation in Mus musculus The majority of these genes were not previously known to support immune function or homeostasis. Mouse geneticists will find CE data informative in identifying causative mutations within quantitative trait loci, while clinical geneticists may use CE to help connect causative variants with rare heritable diseases of immunity, even in the absence of linkage information. CE displays integrated mutation, phenotype, and linkage data, and is freely available for query online.

Multi-Task Foreground-Aware Network with Depth Completion for Enhanced RGB-D Fusion Object Detection Based on Transformer.

Fusing multiple sensor perceptions, specifically LiDAR and camera, is a prevalent method for target recognition in autonomous driving systems. Traditional object detection algorithms are limited by the sparse nature of LiDAR point clouds, resulting in poor fusion performance, especially for detecting small and distant targets. In this paper, a multi-task parallel neural network based on the Transformer is constructed to simultaneously perform depth completion and object detection. The loss functions are redesigned to reduce environmental noise in depth completion, and a new fusion module is designed to enhance the network's perception of the foreground and background. The network leverages the correlation between RGB pixels for depth completion, completing the LiDAR point cloud and addressing the mismatch between sparse LiDAR features and dense pixel features. Subsequently, we extract depth map features and effectively fuse them with RGB features, fully utilizing the depth feature differences between foreground and background to enhance object detection performance, especially for challenging targets. Compared to the baseline network, improvements of 4.78%, 8.93%, and 15.54% are achieved in the difficult indicators for cars, pedestrians, and cyclists, respectively. Experimental results also demonstrate that the network achieves a speed of 38 fps, validating the efficiency and feasibility of the proposed method.

[Highly polar chemical constituents from whole herb of Scindapsus officinalis].

Macroporous resin column chromatography, MCI medium pressure column chromatography, and semi-preparative high performance liquid chromatography were employed to isolate the chemical components from the aqueous extract of the whole herb of Scindapsus officinalis. The structures of the compounds were identified based on the physical and chemical properties and the spectroscopic data. Ten compounds were isolated from the aqueous extract and identified as 3,4-dihydroxyphenylethyl-8-O-[ß-D-apiofuranosyl-(1→4)]-ß-D-glucopyranoside(1), alternamide B(2), 3,4-dihydroxyphenylethyl-O-ß-D-glucopyranoside(3), 1-(4-hydroxy)-phenylethyl-ß-D-galactopyranoside(4), 3,4-dihydroxyphenylethyl-8-O-[ß-D-apiofuranosyl-(1→2)]-ß-D-glucopyranoside(5), hydroxytyrosol-4-O-ß-D-glucopyranoside(6), 3,5-dihydroxyphenylethyl-3-O-ß-D-glucopyranoside(7), salidroside(8), dihydroisoquinolone(9), and 4-methoxybenzenepropanol-3-O-ß-D-glucopyranoside(10). Among them, compound 1 was a new one, and compounds 2-10 were obtained from S. officinalis for the first time. The RAW264.7 cells were exposed to lipopolysaccharide for the mode-ling of inflammation, and the cells were then used to examine anti-inflammatory activities of the compounds. The results showed that compounds 6 and 7 had strong anti-inflammatory activities, while compounds 1, 2, and 5 had moderate anti-inflammatory activities.

Methionine deficiency facilitates antitumour immunity by altering m6A methylation of immune checkpoint transcripts.

OBJECTIVE: Methionine metabolism is involved in a myriad of cellular functions, including methylation reactions and redox maintenance. Nevertheless, it remains unclear whether methionine metabolism, RNA methylation and antitumour immunity are molecularly intertwined. DESIGN: The antitumour immunity effect of methionine-restricted diet (MRD) feeding was assessed in murine models. The mechanisms of methionine and YTH domain-containing family protein 1 (YTHDF1) in tumour immune escape were determined in vitro and in vivo. The synergistic effects of MRD or YTHDF1 depletion with PD-1 blockade were also investigated. RESULTS: We found that dietary methionine restriction reduced tumour growth and enhanced antitumour immunity by increasing the number and cytotoxicity of tumour-infiltrating CD8+ T cells in different mouse models. Mechanistically, the S-adenosylmethionine derived from methionine metabolism promoted the N6-methyladenosine (m6A) methylation and translation of immune checkpoints, including PD-L1 and V-domain Ig suppressor of T cell activation (VISTA), in tumour cells. Furthermore, MRD or m6A-specific binding protein YTHDF1 depletion inhibited tumour growth by restoring the infiltration of CD8+ T cells, and synergised with PD-1 blockade for better tumour control. Clinically, YTHDF1 expression correlated with poor prognosis and immunotherapy outcomes for cancer patients. CONCLUSIONS: Methionine and YTHDF1 play a critical role in anticancer immunity through regulating the functions of T cells. Targeting methionine metabolism or YTHDF1 could be a potential new strategy for cancer immunotherapy.

Fluorescence Imaging of Intracellular Glutathione Levels in the Endoplasmic Reticulum to Reveal the Inhibition Effect of Rutin on Ferroptosis.

Ferroptosis is an emerging form of nonapoptotic cell death, and the search for novel ferroptosis inhibitors is of great importance to explore unique cytoprotective strategies against ferroptosis-relevant diseases. In this work, we present an endoplasmic reticulum-targeting fluorescent probe (ER-G) for the imaging of intracellular glutathione (GSH) levels and revealed the inhibition effect of rutin on ferroptosis. Structurally, ER-G utilized a cyclohexyl sulfonylurea as the endoplasmic reticulum-targeting unit, and single-crystal X-ray diffraction analysis confirmed that ER-G possessed a N-oxide pyridine sulfinyl group instead of sulfone. After the response of ER-G to GSH, the fluorescence intensity at 523 nm displayed a significant increase by 3900-fold. ER-G showed extreme sensitivity and selectivity to GSH. The fluorescence imaging results demonstrated that ER-G exhibited excellent endoplasmic reticulum-targeting properties and could be applied to monitor GSH levels in the endoplasmic reticulum during the erastin-induced ferroptosis process. By the fluorescence imaging of GSH levels in the endoplasmic reticulum, it was demonstrated that rutin could efficiently block the depletion of GSH during erastin-induced ferroptosis and potentially act as a novel ferroptosis inhibitor. Moreover, unlike traditional ferroptosis inhibitors, it was speculated that the inhibition mechanism of rutin to ferroptosis was the integration of the chelate effect on Fe(II) ions and antioxidant effect. We expect that fluorescence imaging of GSH levels in the endoplasmic reticulum could provide a convenient and feasible method to evaluate the inhibition effect of small molecules on ferroptosis.

Image distortion by ambiguous multiple-photon detections in a superconducting nanowire single-photon imager and the correction method.

Scaling up superconducting nanowire single-photon detectors (SNSPDs) into a large array for imaging applications is the current pursuit. Although various readout architectures have been proposed, they cannot resolve multiple-photon detections (MPDs) currently, which limits the operation of the SNSPD arrays at high photon flux. In this study, we focused on the readout ambiguity of a superconducting nanowire single-photon imager applying time-of-flight multiplexing readout. The results showed that image distortion depended on both the incident photon flux and the imaging object. By extracting multiple-photon detections on idle pixels, which were virtual because of the incorrect mapping from the ambiguous readout, a correction method was proposed. An improvement factor of 1.3~9.3 at a photon flux of µ = 5 photon/pulse was obtained, which indicated that joint development of the pixel design and restoration algorithm could compensate for the readout ambiguity and increase the dynamic range.

Development of an Endoplasmic Reticulum-targeting Fluorescent Probe for the Imaging of Superoxide Anion in Living Cells.

Superoxide anion (O2•-) is an important reactive oxygen species (ROS), and plays critical roles in biological systems. ER stress has close relation with many metabolic diseases, and could lead to the abnormal production of ROS including O2•-. Herein, we present an ER-targeting probe (ER-Tf) for the detection of O2•- in living cells. The probe ER-Tf used triflate as the response site for O2•-, and employed p-methylbenzenesulfonamide as ER-targeting moiety. In response to O2•-, the triflate of the probe ER-Tf converted to hydroxyl group, providing strong blue emission under the excitation of ultraviolet light. The probe ER-Tf exhibited high sensitivity and selectivity to O2•-. Bioimaging experiments showed that the probe ER-Tf can be applied to detect O2•- at ER, and also demonstrated that rotenone could increase the generation of O2•- in living cells, while the O2•- level at ER showed no remarkable change during ferroptosis.

TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function.

T cells and the T-cell receptor (TCR) repertoire play pivotal roles in immune response and immunotherapy. TCR sequencing (TCR-Seq) technology has enabled accurate profiling TCR repertoire and currently a large number of TCR-Seq data are available in public. Based on the urgent need to effectively re-use these data, we developed TCRdb, a comprehensive human TCR sequences database, by a uniform pipeline to characterize TCR sequences on TCR-Seq data. TCRdb contains more than 277 million highly reliable TCR sequences from over 8265 TCR-Seq samples across hundreds of tissues/clinical conditions/cell types. The unique features of TCRdb include: (i) comprehensive and reliable sequences for TCR repertoire in different samples generated by a strict and uniform pipeline of TCRdb; (ii) powerful search function, allowing users to identify their interested TCR sequences in different conditions; (iii) categorized sample metadata, enabling comparison of TCRs in different sample types; (iv) interactive data visualization charts, describing the TCR repertoire in TCR diversity, length distribution and V-J gene utilization. The TCRdb database is freely available at http://bioinfo.life.hust.edu.cn/TCRdb/ and will be a useful resource in the research and application community of T cell immunology.

On-Chip Compressive Sensing with a Single-Photon Avalanche Diode Array.

Single-photon avalanche diodes (SPADs) are novel image sensors that record photons at extremely high sensitivity. To reduce both the required sensor area for readout circuits and the data throughput for SPAD array, in this paper, we propose a snapshot compressive sensing single-photon avalanche diode (CS-SPAD) sensor which can realize on-chip snapshot-type spatial compressive imaging in a compact form. Taking advantage of the digital counting nature of SPAD sensing, we propose to design the circuit connection between the sensing unit and the readout electronics for compressive sensing. To process the compressively sensed data, we propose a convolution neural-network-based algorithm dubbed CSSPAD-Net which could realize both high-fidelity scene reconstruction and classification. To demonstrate our method, we design and fabricate a CS-SPAD sensor chip, build a prototype imaging system, and demonstrate the proposed on-chip snapshot compressive sensing method on the MINIST dataset and real handwritten digital images, with both qualitative and quantitative results.

Endoplasmic Reticulum Stress and Mitochondrial Stress in Drug-Induced Liver Injury.

Drug-induced liver injury (DILI) is a widespread and harmful disease closely linked to mitochondrial and endoplasmic reticulum stress (ERS). Globally, severe drug-induced hepatitis, cirrhosis, and liver cancer are the primary causes of liver-related morbidity and mortality. A hallmark of DILI is ERS and changes in mitochondrial morphology and function, which increase the production of reactive oxygen species (ROS) in a vicious cycle of mutually reinforcing stress responses. Several pathways are maladapted to maintain homeostasis during DILI. Here, we discuss the processes of liver injury caused by several types of drugs that induce hepatocyte stress, focusing primarily on DILI by ERS and mitochondrial stress. Importantly, both ERS and mitochondrial stress are mediated by the overproduction of ROS, destruction of Ca2+ homeostasis, and unfolded protein response (UPR). Additionally, we review new pathways and potential pharmacological targets for DILI to highlight new possibilities for DILI treatment and mitigation.

Efficient separation of anti-inflammatory isolates from Polygonti rhizome by three different modes of high-speed counter-current chromatography.

Successful isolation of 15 compounds from Polygonti rhizome was obtained by an efficient technique combined with macroporous resin column chromatography pretreatment and three different modes of high-speed counter-current chromatography for the first time. For the pretreatment, AB-8 resin was applied to remove the polysaccharides and enrich four different parts (samples I, II, III, and IV) by polarities. For the separation, sample I was separated by pH-zone-refining counter-current chromatography and seven cycle recycling mode high-speed counter-current chromatography, yielding four alkaloids (1--4); samples II-IV were further separated by the conventional high-speed counter-current chromatography, yielding seven flavonoids (5-10, 12), one steroid saponin (11), and three terpenoids (13-15). Finally, the isolates were assayed for their anti-inflammatory activities against nitric oxide production with compounds 5, 9-10, 13 showing significant anti-inflammatory activities, IC50 values which were 13.0, 16.2, 17.1, and 14.7 µM, respectively, while others showing moderate and weak anti-inflammatory activities, respectively.

Enhanced susceptibility to chemically induced colitis caused by excessive endosomal TLR signaling in LRBA-deficient mice.

LPS-responsive beige-like anchor (LRBA) protein deficiency in humans causes immune dysregulation resulting in autoimmunity, inflammatory bowel disease (IBD), hypogammaglobulinemia, regulatory T (Treg) cell defects, and B cell functional defects, but the cellular and molecular mechanisms responsible are incompletely understood. In an ongoing forward genetic screen for N-ethyl-N-nitrosourea (ENU)-induced mutations that increase susceptibility to dextran sodium sulfate (DSS)-induced colitis in mice, we identified two nonsense mutations in Lrba Although Treg cells have been a main focus in LRBA research to date, we found that dendritic cells (DCs) contribute significantly to DSS-induced intestinal inflammation in LRBA-deficient mice. Lrba-/- DCs exhibited excessive IRF3/7- and PI3K/mTORC1-dependent signaling and type I IFN production in response to the stimulation of the Toll-like receptors (TLRs) 3, TLR7, and TLR9. Substantial reductions in cytokine expression and sensitivity to DSS in LRBA-deficient mice were caused by knockout of Unc93b1, a chaperone necessary for trafficking of TLR3, TLR7, and TLR9 to endosomes. Our data support a function for LRBA in limiting endosomal TLR signaling and consequent intestinal inflammation.