Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection.

Identification of host genes essential for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may reveal novel therapeutic targets and inform our understanding of coronavirus disease 2019 (COVID-19) pathogenesis. Here we performed genome-wide CRISPR screens in Vero-E6 cells with SARS-CoV-2, Middle East respiratory syndrome CoV (MERS-CoV), bat CoV HKU5 expressing the SARS-CoV-1 spike, and vesicular stomatitis virus (VSV) expressing the SARS-CoV-2 spike. We identified known SARS-CoV-2 host factors, including the receptor ACE2 and protease Cathepsin L. We additionally discovered pro-viral genes and pathways, including HMGB1 and the SWI/SNF chromatin remodeling complex, that are SARS lineage and pan-coronavirus specific, respectively. We show that HMGB1 regulates ACE2 expression and is critical for entry of SARS-CoV-2, SARS-CoV-1, and NL63. We also show that small-molecule antagonists of identified gene products inhibited SARS-CoV-2 infection in monkey and human cells, demonstrating the conserved role of these genetic hits across species. This identifies potential therapeutic targets for SARS-CoV-2 and reveals SARS lineage-specific and pan-CoV host factors that regulate susceptibility to highly pathogenic CoVs.

OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.

AlphaFold2 revolutionized structural biology with the ability to predict protein structures with exceptionally high accuracy. Its implementation, however, lacks the code and data required to train new models. These are necessary to (1) tackle new tasks, like protein-ligand complex structure prediction, (2) investigate the process by which the model learns and (3) assess the model's capacity to generalize to unseen regions of fold space. Here we report OpenFold, a fast, memory efficient and trainable implementation of AlphaFold2. We train OpenFold from scratch, matching the accuracy of AlphaFold2. Having established parity, we find that OpenFold is remarkably robust at generalizing even when the size and diversity of its training set is deliberately limited, including near-complete elisions of classes of secondary structure elements. By analyzing intermediate structures produced during training, we also gain insights into the hierarchical manner in which OpenFold learns to fold. In sum, our studies demonstrate the power and utility of OpenFold, which we believe will prove to be a crucial resource for the protein modeling community.

KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements.

Tumours use various strategies to evade immune surveillance1,2. Immunotherapies targeting tumour immune evasion such as immune checkpoint blockade have shown considerable efficacy on multiple cancers3,4 but are ineffective for most patients due to primary or acquired resistance5-7. Recent studies showed that some epigenetic regulators suppress anti-tumour immunity2,8-12, suggesting that epigenetic therapies could boost anti-tumour immune responses and overcome resistance to current immunotherapies. Here we show that, in mouse melanoma models, depletion of KDM5B-an H3K4 demethylase that is critical for melanoma maintenance and drug resistance13-15-induces robust adaptive immune responses and enhances responses to immune checkpoint blockade. Mechanistically, KDM5B recruits the H3K9 methyltransferase SETDB1 to repress endogenous retroelements such as MMVL30 in a demethylase-independent manner. Derepression of these retroelements activates cytosolic RNA-sensing and DNA-sensing pathways and the subsequent type-I interferon response, leading to tumour rejection and induction of immune memory. Our results demonstrate that KDM5B suppresses anti-tumour immunity by epigenetic silencing of retroelements. We therefore reveal roles of KDM5B in heterochromatin regulation and immune evasion in melanoma, opening new paths for the development of KDM5B-targeting and SETDB1-targeting therapies to enhance tumour immunogenicity and overcome immunotherapy resistance.

Mechanochemical upcycling of spent LiCoO2 to new LiNi0.80Co0.15Al0.05O2 battery: An atom economy strategy.

The use of strong acids and low atom efficiency in conventional hydrometallurgical recycling of spent lithium-ion batteries (LIBs) results in significant secondary wastes and CO2 emissions. Herein, we utilize the waste metal current collectors in spent LIBs to promote atom economy and reduce chemicals consumption in a conversion process of spent Li1-xCoO2 (LCO) → new LiNi0.80Co0.15Al0.05O2 (NCA) cathode. Mechanochemical activation is employed to achieve moderate valence reduction of transition metal oxides (Co3+→Co2+,3+) and efficient oxidation of current collector fragments (Al0→Al3+, Cu0→Cu1+,2+), and then due to stored internal energy from ball-milling, the leaching rates of Li, Co, Al, and Cu in the ≤4 mm crushed products uniformly approach 100% with just weak acetic acid. Instead of corrosive precipitation reagents, larger Al fragments (≥4 mm) are used to control the oxidation/reduction potential (ORP) in the aqueous leachate and induce the targeted removal of impurity ions (Cu, Fe). After the upcycling of NCA precursor solution to NCA cathode powders, we demonstrate excellent electrochemical performance of the regenerated NCA cathode and improved environmental impact. Through life cycle assessments, the profit margin of this green upcycling path reaches about 18%, while reducing greenhouse gas emissions by 45%.

Long-term oncological outcomes of robotic versus laparoscopic gastrectomy for gastric cancer: multicentre cohort study.

BACKGROUND: The aim of this multicentre cohort study was to compare the long-term oncological outcomes of robotic gastrectomy (RG) and laparoscopic gastrectomy (LG) for patients with gastric cancer. METHODS: Patients with gastric cancer who underwent radical gastrectomy by robotic or laparoscopic approaches from 1 March 2010 to 31 December 2018 at 10 high-volume centres in China were selected from institutional databases. Patients receiving RG were matched 1 : 1 by propensity score with patients undergoing LG. The primary outcome was 3-year disease-free survival. Secondary outcomes were overall survival and disease recurrence. RESULTS: Some 2055 patients who underwent RG and 4309 patients who had LG were included. The propensity score-matched cohort comprised 2026 RGs and 2026 LGs. Median follow-up was 41 (i.q.r. 39-58) months for the RG group and 39 (38-56) months for the LG group. The 3-year disease-free survival rates were 80.8% in the RG group and 79.5% in the LG group (log rank P = 0.240; HR 0.92, 95% c.i. 0.80 to 1.06; P = 0.242). Three-year OS rates were 83.9 and 81.8% respectively (log rank P = 0.068; HR 0.87, 0.75 to 1.01; P = 0.068) and the cumulative incidence of recurrence over 3 years was 19.3% versus 20.8% (HR 0.95, 0.88 to 1.03; P = 0.219), with no difference between groups. CONCLUSION: RG and LG in patients with gastric cancer are associated with comparable disease-free and overall survival.

Uridine diphosphate glucosyltransferase is vital for fenpropathrin resistance in Bombyx mori (Lepidoptera).

The silkworm (Bombyx mori) is an important model lepidopteran insect and can be used to identify pesticide resistance-related genes of great significance for biological control of pests. Uridine diphosphate glucosyltransferases (UGTs), found in all organisms, are the main secondary enzymes involved in the metabolism of heterologous substances. However, it remains uncertain if silkworm resistance to fenpropathrin involves UGT. This study observes significant variations in BmUGT expression among B. mori strains with variable fenpropathrin resistance post-feeding, indicating BmUGT's role in fenpropathrin detoxification. Knockdown of BmUGT with RNA interference and overexpression of BmUGT significantly decreased and increased BmN cell activity, respectively, indicating that BmUGT plays an important role in the resistance of silkworms to fenpropathrin. In addition, fenpropathrin residues were significantly reduced after incubation for 12 h with different concentrations of a recombinant BmUGT fusion protein. Finally, we verified the conservation of UGT to detoxify fenpropathrin in Spodoptera exigua: Its resistance to fenpropathrin decreased significantly after knocking down SeUGT. In a word, UGT plays an important role in silkworm resistance to fenpropathrin by directly degrading the compound, a function seen across other insects. The results of this study are of great significance for breeding silkworm varieties with high resistance and for biological control of pests.

A robust method for simultaneous determination of eight B vitamins in human serum by liquid chromatography tandem mass spectrometry.

The level of vitamin B group in human serum is an important index of human health. Among B vitamins, cyanocobalamin in serum is unstable and its content is extremely low. Rapid and simultaneous detection of multiple B vitamins including cyanocobalamin is a challenge. Herein, we have developed a rapid and stable method that can realize the determination of thiamine, riboflavin, nicotinamide, pantothenic acid, pyridoxic acid, biotin, 5-methyltetrahydrofolate, and cyanocobalamin simultaneously in 6 min. The method was established based on protein precipitation with methanol and then chromatographic separation was achieved using Waters acquity ultra-high-performance liquid chromatography high strength silica T3 column, which was stable and sensitive especially for cyanocobalamin. Limit of quantification, precision, trueness, and matrix effect were validated according to the European Medicines Agency and United States Food and Drug guidelines and Clinical and Laboratory Standards Institute guidelines on bioanalytical method. The limit of quantification for thiamine, riboflavin, nicotinamide, pantothenic acid, pyridoxic acid, biotin, 5-methyltetrahydrofolate, and cyanocobalamin was 0.4, 0.4, 0.8, 2.0, 0.4, 0.1, 0.4, and 0.04 ng/mL separately, respectively. Intra- and interday precisions were 1.1%-12.4% and 2.0%-13.5%, respectively. The relative errors were between 0.3% and 13.3%, and the matrix effects were between 2.6% and 10.4%.

POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins.

RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation. Accurate identification of RBP binding sites in multiple cell lines and tissue types from diverse species is a fundamental endeavor towards understanding the regulatory mechanisms of RBPs under both physiological and pathological conditions. Our POSTAR annotation processes make use of publicly available large-scale CLIP-seq datasets and external functional genomic annotations to generate a comprehensive map of RBP binding sites and their association with other regulatory events as well as functional variants. Here, we present POSTAR3, an updated database with improvements in data collection, annotation infrastructure, and analysis that support the annotation of post-transcriptional regulation in multiple species including: we made a comprehensive update on the CLIP-seq and Ribo-seq datasets which cover more biological conditions, technologies, and species; we added RNA secondary structure profiling for RBP binding sites; we provided miRNA-mediated degradation events validated by degradome-seq; we included RBP binding sites at circRNA junction regions; we expanded the annotation of RBP binding sites, particularly using updated genomic variants and mutations associated with diseases. POSTAR3 is freely available at http://postar.ncrnalab.org.

Density of States and Spectral Function of a Superconductor out of a Quantum-Critical Metal.

We analyze the validity of a quasiparticle description of a superconducting state above a metallic quantum-critical point (QCP). A normal state at a QCP is a non-Fermi liquid with no coherent quasiparticles. A superconducting order gaps out low-energy excitations, except for a sliver of states for non-s-wave gap symmetry, and at a first glance, restores coherent quasiparticle behavior. We argue that this does not necessarily hold as the fermionic self-energy may remain singular above the gap edge. This singularity gives rise to markedly non-BCS behavior of the density of states and to the appearance of a nondispersing mode at the gap edge in the spectral function. We analyze the set of quantum-critical models with an effective dynamical four-fermion interaction V(Ω)∝1/Ω^{γ}, where Ω is a frequency of a boson, which mediates the interaction. We show that coherent quasiparticle behavior in a superconducting state holds for γ<1/2, but breaks down for larger γ. We discuss signatures of quasiparticle breakdown and compare our results with the photoemission data for Bi2201 and Bi2212.

Rh(III)-Catalyzed C-H Functionalization/Annulation of 1-Arylindazolones: Divergent Synthesis of Fused Indazolones and Allyl Indazolones.

Rh(III)-catalyzed C-H/N-H annulation and C-H allylation of phenylindazolones have been realized by employing 5-methylene-1,3-dioxan-2-one and 4-vinyl-1,3-dioxolan-2-one as scalable cross-coupling partners, delivering functionalized indazolone fused heterocycles and branched and linear allyl indazolones respectively in moderate to high yield. These divergent synthesis protocols showcase mild conditions, broad substrate scope, and high functional-group compatibility. In addition, scale-up synthesis and preliminary mechanistic exploratory were also accomplished.

Synthesis of Indole-Substituted Trifluoromethyl Sulfonium Ylides by Cp*Rh(III)-Catalyzed Diazo-carbenoid Addition to Trifluoromethylthioether.

The indole-substituted trifluoromethyl sulfonium ylide has been developed via Cp*Rh(III)-catalyzed diazo-carbenoid addition to trifluoromethylthioether and is the first example of an Rh(III)-catalyzed diazo-carbenoid addition reaction with trifluoromethylthioether. Several kinds of indole-substituted trifluoromethyl sulfonium ylide were constructed under mild reaction conditions. The reported method exhibited high functional group compatibility and broad substrate scope. In addition, the protocol was found to be complementary to the method disclosed by a Rh(II) catalyst.

KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic.

The histone lysine demethylase 5 (KDM5) family proteins are Fe2+ and α-ketoglutarate-dependent dioxygenases, with jumonji C (JmjC) domain as their catalytic core and several plant homeodomains (PHDs) to bind different histone methylation marks. These enzymes are capable of demethylating tri-, di- and mono-methylated lysine 4 in histone H3 (H3K4me3/2/1), the key epigenetic marks for active chromatin. Thus, this H3K4 demethylase family plays critical roles in cell fate determination during development as well as malignant transformation. KDM5 demethylases have both oncogenic and tumor suppressive functions in a cancer type-dependent manner. In solid tumors, KDM5A/B are generally oncogenic, whereas KDM5C/D have tumor suppressive roles. Their involvement in de-differentiation, cancer metastasis, drug resistance, and tumor immunoevasion indicated that KDM5 family proteins are promising drug targets for cancer therapy. Significant efforts from both academia and industry have led to the development of potent and selective KDM5 inhibitors for preclinical experiments and phase I clinical trials. However, a better understanding of the roles of KDM5 demethylases in different physiological and pathological conditions is critical for further developing KDM5 modulators for clinical applications.

A Robust Metal-Organic Framework with Scalable Synthesis and Optimal Adsorption and Desorption for Energy-Efficient Ethylene Purification.

Adsorptive separation is an energy-efficient alternative, but its advancement has been hindered by the challenge of industrially potential adsorbents development. Herein, a novel ultra-microporous metal-organic framework ZU-901 is designed that satisfies the basic criteria raised by ethylene/ethane (C2 H4 /C2 H6 ) pressure swing adsorption (PSA). ZU-901 exhibits an "S" shaped C2 H4 curve with high sorbent selection parameter (65) and could be mildly regenerated. Through green aqueous-phase synthesis, ZU-901 is easily scalable with 99 % yield, and it is stable in water, acid, basic solutions and cycling breakthrough experiments. Polymer-grade C2 H4 (99.51 %) could be obtained via a simulating two-bed PSA process, and the corresponding energy consumption is only 1/10 of that of simulating cryogenic distillation. Our work has demonstrated the great potential of pore engineering in designing porous materials with desired adsorption and desorption behavior to implement an efficient PSA process.

Lumi-HOF@Tb as Probes for Multiple Ratiometric Fluorescence and Chemiluminescence Sensing of α-Glucosidase.

The innovative assembly of luminescent hydrogen-bonded organic frameworks (HOFs) into multifunctional optical sensors is of great significance for developing advanced materials. Herein, we report a facile room-temperature synthesis strategy for the luminol HOF modified by Tb3+ (Lumi-HOF@Tb) and featuring sensitive chemiluminescence and fluorescence characteristics. Lumi-HOF@Tb is further pioneered as a dual-signal sensor for selective detection of α-glucosidase, a type of enzyme that plays a crucial role in the digestion of carbohydrates, and screening of its inhibitors. The sensor is constructed by combining the dual optical characteristics of luminol from the HOF and lanthanide ion assistance. From the hydrolysis of α-glucosidase and the 4-nitrophenyl-α-d-glucopyranoside (pNGP) substrate emerges the fluorescent luminol-p-nitrophenol (pNP) complex at 466 nm and changes the inner filter absorption to recover Tb3+ characteristic fluorescence at 546 nm; luminol also produces a chemiluminescence signal driven by H2O2 from additional glucose oxidase-catalyzed hydrolysis of α-d-glucose. Fluorescence and chemiluminescence assays for α-glucosidase activity have therefore been established and exhibit detection limits as low as 0.04 and 0.005 U L-1, respectively. This study not only presents the possibility of Ln3+-HOF-based sensors as intelligent optical materials by integration of fluorescence and chemiluminescence techniques but also demonstrates great potential for future applications in biosensing.

Rhodium(III)-catalyzed regioselective C(sp2)-H activation of indoles at the C4-position with iodonium ylides.

Herein, we report a Rh(III)-catalyzed C4-selective activation of indoles by using iodonium ylides as carbene precursors. This protocol proceeded under redox neutral reaction conditions and provided important coupling products with good tolerance of functional groups and high yields. In addition, one-pot synthesis and scale-up and mechanistic studies were also conducted.

Thioether-directed Rh(III)-catalyzed peri-selective acyloxylation of arenes.

A thioether directed acyloxylation of arenes has been realized via Cp*Rh(III)-catalyzed C-H activation and subsequent coupling with carboxylic acids. This new method showed high functional group compatibility and broad substrate scope. Primary mechanistic studies have been conducted and a tentative reaction mechanism was proposed. It represents the first example of a thioether-directed Cp*Rh(III)-catalyzed C(sp2)-H acyloxylation reaction.

Development of a miniaturized and modular probe for fNIRS instrument.

Functional near-infrared spectroscopy (fNIRS) is a non-invasive and promising method for continuously monitoring hemodynamic and metabolic changes in tissues. However, the existing fNIRS equipment uses optical fiber, which is bulky, expensive, and time-consuming. We present a miniaturized, modular, novel silicon photomultiplier (SiPM) detector and develop a fNIRS instrument aimed at investigating the cerebral hemodynamic response for patients with epilepsy. Light emitting probe is a circle with a diameter of 5 mm. Independent and modular light source and detector are more flexible in placement. The system can be expanded to high-density measurement with 16 light sources, 16 detectors, and 52 channels. The sampling rate of each channel is 25 Hz. Instrument performance was evaluated using brain tissue phantom and in vivo experiments. High signal-to-noise ratio (60 dB) in source detector separation (SDS) of 30 mm, good stability (0.1%), noise equivalent power (0.89 pW), and system drift (0.56%) were achieved in the phantom experiment. Forearm blood-flow occlusion experiments were performed on the forearm of three healthy volunteers to demonstrate the ability to track rapid hemodynamic changes. Breath holding experiments on the forehead of healthy volunteers demonstrated the system can well detect brain function activity. The computer software was developed to display the original light signal intensity and the concentration changes of oxygenated hemoglobin (HbO2) and deoxygenated hemoglobin (HbR) in real time. This system paves the way for our further diagnosis of epilepsy.

Observation of 4- and 6-Magnon Bound States in the Spin-Anisotropic Frustrated Antiferromagnet FeI_{2}.

We observe a wealth of multimagnon bound states in the strongly anisotropic spin-1 triangular antiferromagnet FeI_{2} using time-domain terahertz spectroscopy. These unconventional excitations can arise in ordered magnets due to attractive magnon-magnon interactions and alter their properties. We analyze the energy-magnetic field spectrum via an exact diagonalization method for a dilute gas of interacting magnons and detect up to 4- and 6-magnon bound states, hybridized with single magnons. This zoo of tunable interacting quasiparticles provides a unique platform to study decay and renormalization, reminiscent of the few-body problems found in cold-atom, nuclear, and particle physics.

Upgrading Octane Number of Naphtha by a Robust and Easily Attainable Metal-Organic Framework through Selective Molecular Sieving of Alkane Isomers.

The separation of alkanes, particularly monobranched and dibranched isomers, is of paramount importance in the petrochemical industry for optimizing the feedstock of ethylene production as well as for upgrading the octane number of gasoline. Here, we report the full separation of linear/monobranched alkanes from their dibranched isomers by a robust and easily scalable metal-organic framework material, Co3 (HCOO)6 . The compound completely excludes dibranched alkanes but adsorbs their linear and monobranched isomers, as evidenced by single-component and multicomponent adsorption measurements. More importantly, the material exhibits excellent performance in separating naphtha and is capable of providing high quality feedstock for the production of ethylene and gasoline components with high octane number, making it a promising candidate for naphtha separation in petrochemical industry.

Mild Synthesis of 3,4-Dihydroisoquinolin-1(2H)-ones via Rh(III)-Catalyzed Tandem C-H-Allylation/N-Alkylation Annulation with 2-Methylidenetrimethylene Carbonate.

A tandem rhodium(III)-catalyzed system was established to access 3,4-dihydroisoquinolin-1(2H)-one by coupling of N-methoxy-3-methylbenzamide with 2-methylidenetrimethylene carbonate. This one-pot synthesis protocol processed smoothly under mild reaction conditions. Moreover, a total of 28 examples, broad substrate scope, and high functional-group compatibility were observed. Preliminary mechanism studies were also conducted and demonstrated that the rhodium(III) catalyst played a vital role in the C-H-allylation and N-alkylation cyclization process.