DeepCheck: multitask learning aids in assessing microbial genome quality.

Metagenomic analyses facilitate the exploration of the microbial world, advancing our understanding of microbial roles in ecological and biological processes. A pivotal aspect of metagenomic analysis involves assessing the quality of metagenome-assembled genomes (MAGs), crucial for accurate biological insights. Current machine learning-based methods often treat completeness and contamination prediction as separate tasks, overlooking their inherent relationship and limiting models' generalization. In this study, we present DeepCheck, a multitasking deep learning framework for simultaneous prediction of MAG completeness and contamination. DeepCheck consistently outperforms existing tools in accuracy across various experimental settings and demonstrates comparable speed while maintaining high predictive accuracy even for new lineages. Additionally, we employ interpretable machine learning techniques to identify specific genes and pathways that drive the model's predictions, enabling independent investigation and assessment of these biological elements for deeper insights.

PB-LKS: a python package for predicting phage-bacteria interaction through local K-mer strategy.

Bacteriophages can help the treatment of bacterial infections yet require in-silico models to deal with the great genetic diversity between phages and bacteria. Despite the tolerable prediction performance, the application scope of current approaches is limited to the prediction at the species level, which cannot accurately predict the relationship of phages across strain mutants. This has hindered the development of phage therapeutics based on the prediction of phage-bacteria relationships. In this paper, we present, PB-LKS, to predict the phage-bacteria interaction based on local K-mer strategy with higher performance and wider applicability. The utility of PB-LKS is rigorously validated through (i) large-scale historical screening, (ii) case study at the class level and (iii) in vitro simulation of bacterial antiphage resistance at the strain mutant level. The PB-LKS approach could outperform the current state-of-the-art methods and illustrate potential clinical utility in pre-optimized phage therapy design.

Correction: The interferon stimulated gene 20 protein (ISG20) is an innate defense antiviral factor that discriminates self versus non-self translation.

[This corrects the article DOI: 10.1371/journal.ppat.1008093.].

Engineering of Cerium Modified TiNb2O7 Nanoparticles For Low-Temperature Lithium-Ion Battery.

Although TiNb2O7 (TNO) with comparable operating potential and ideal theoretical capacity is considered to be the most ideal replacement for negative Li4Ti5O12 (LTO), the low ionic and electronic conductivity still limit its practical application as satisfactory anode for lithium-ion batteries (LIBs) with high-power density. Herein, TNO nanoparticles modified by Cerium (Ce) with outstanding electrochemical performance are synthesized. The successful introduction of Ce3+ in the lattice leads to increased interplanar spacing, refined grain size, more oxygen vacancy, and a smaller lithium diffusion barrier, which are conducive to improve conductivity of both Li+ and electrons. As a result, the modified TNO reaches high reversible capacity of 256.0 mA h g-1 at 100 mA g-1 after 100 cycles, and 183.0 mA h g-1 even under 3200 mA g-1. In particular, when the temperature drops to -20 °C, the cell undergoing 1500 cycles at a high current density of 500 mA g-1 can still reach 89.7 mA h g-1, corresponding to a capacity decay rate per cycle of only 0.033%. This work provides a new way to improve the electrochemical properties of alternative anodes for LIBs at extreme temperature.

Design, synthesis and biological evaluation of tanshinone IIA derivatives as NLRP3 inflammasome inhibitors.

Natural product structures have long provided valuable pharmacophores and even candidates for drug discovery. Tanshinone scaffold showed moderately inhibitory activity in NLRP3 inflammasome/IL-1ß pathway. Herein, we designed a series of derivatives on different regions of Tanshinone IIA (TNA) scaffold. The biological evaluation identified compound T10, a scaffold hybrid of TNA and salicylic acid, as a potent NLRP3 inflammasome inhibitor. Mechanistically, T10 inhibits the production of ROS and prevents NLRP3 inflammasome-dependent IL-1ß production. In addition, treatment with T10 significantly attenuated inflammatory response in DSS-induced peritonitis. Our work describes a potential tanshinone-based derivative, which needs to be further structurally optimized as NLRP3 inflammasome inhibitors for treating inflammatory disorders.

Rapid Bacteriophage Quantification by Digital Biosensing on a SlipChip Microfluidic Device.

The rise of antimicrobial resistance (AMR) is a major global public health concern, and it is urgent to develop new antimicrobial drugs and alternative therapies. There has been growing interest in the use of phage therapy as an alternative to treat AMR, and it has shown promising results in early studies and clinical trials. Phage quantification is a crucial step in the development and application of phage therapy. The traditional double-layer plaque assay requires cumbersome manual operations and typically takes up to 18 h to yield a rough phage estimation. Spectrophotometry, flow cytometry, and PCR-based methods cannot distinguish between infectious and noninfectious phages. Here, we developed a digital biosensing method for rapid bacteriophage quantification on a digital phage SlipChip (dp-SlipChip) microfluidic device containing 2304 microdroplets in 3 nL. By compartmentalizing the phages and bacteria in nanoliter droplets and analyzing the growth profile of bacteria at 3 h, the number of infectious phages can be precisely quantified. The results from the dp-SlipChip were consistent with the traditional double-layer plaque assay method and exhibited higher consistency and repeatability. The dp-SlipChip does not require a complex fluidic handling instrument to generate and manipulate droplets. This SlipChip-based digital biosensing method not only provides a promising tool for rapid phage quantification, which is important for the use of phages in clinical practice to treat antimicrobial-resistant bacteria, but can also be used as an ultrasensitive, high-specificity method to detect bacteria. Furthermore, this approach can be applied to other digital biology studies that require analysis at the single-object level.

Promoting Effect of Silver Oxide Nanoparticles on the Oxidation of Bisphenol B by Ferrate(VI).

Bisphenol B (BPB, 2,2-bis(4-hydroxyphenyl) butane), as a substitute for bisphenol A, has been widely detected in the environment and become a potential threat to environmental health. This work found that silver oxide nanoparticles (Ag2O) could greatly promote the removal of BPB by ferrate (Fe(VI)). With the presence of 463 mg/L Ag2O, the amount of Fe(VI) required for the complete removal of 10 µM BPB will be reduced by 70%. Meanwhile, the recyclability and stability of Ag2O have been verified by recycling experiments. The characterization results and in situ electrochemical analyses showed that Ag(II) was produced from Ag(I) in the Fe(VI)-Ag2O system, which has a higher electrode potential to oxidize BPB to enhance its removal. A total of 13 intermediates were identified by high-resolution mass spectrometry, and three main reaction pathways were proposed, including oxygen transfer, bond breaking, and polymerization. Based on the toxicity assessment through the ECOSAR program, it is considered that the presence of Ag2O reduced the toxicity of BPB oxidation intermediates to aquatic organisms. These results would deepen our understanding of the interaction between Fe(VI) and Ag2O, which may provide an efficient and environmentally friendly method for water and wastewater treatment.

A Comparative Study on the Oxidation Mechanisms of Substituted Phenolic Pollutants by Ferrate(VI) through Experiments and Density Functional Theory Calculations.

In this work, the oxidation of five phenolic contaminants by ferrate(VI) was comparatively investigated to explore the possible reaction mechanisms by combined experimental results and theoretical calculations. The second-order rate constants were positively correlated with the energy of the highest occupied molecular orbital. Considering electronic effects of different substituents, the easy oxidation of phenols by ferrate(VI) could be ranked as the electron-donating group (-R) > weak electron-withdrawing group (-X) > strong electron-withdrawing group (-(C═O)-). The contributions of reactive species (Fe(VI), Fe(V)/(IV), and •OH) were determined, and Fe(VI) was found to dominate the reaction process. Four main reaction mechanisms including single-oxygen transfer (SOT), double-oxygen transfer (DOT), •OH attack, and electron-transfer-mediated coupling reaction were proposed for the ferrate(VI) oxidation process. According to density functional theory calculation results, the presence of -(C═O)- was more conducive for the occurrence of DOT and •OH attack reactions than -R and -X, while the tendency of SOT for different substituents was -R > -(C═O)- > -X and that of e--transfer reaction was -R > -X > -(C═O)-. Moreover, the DOT pathway was found in the oxidation of all four substituted phenols, indicating that it may be a common reaction mechanism during the ferrate(VI) oxidation of phenolic compounds.

Polyhedral Oligomeric Silsesquioxane Encountering Tannic Acid: A Mild and Efficient Strategy for Interface Modification on Carbon Fiber Composites.

Designing and controlling the interfacial chemistry and microstructure of the carbon fiber is an important step in the surface modification and preparation of high-performance composites. To address this issue, a tannic acid (TA)/polyhedral oligomeric silsesquioxane (POSS) hybrid microstructure, similar to the topological structure, is designed on the fiber surface by one-pot synthesis under mild conditions. Fourier transform infrared (FT-IR), X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM) show that the functionality and surface roughness of the fiber are significantly broadened. Correspondingly, the tensile strength (TS) of CF-TA/POSS100 and interlaminar shear strength (ILSS) of CF-TA/POSS100-based composites increased by 18 and 34%, respectively. Following that, a failure mechanism study is conducted to demonstrate the interphase structure containing TA/POSS, which is quite critical in optimizing the mechanical performance of the multiscale composites. Moreover, the strategy for the use of TA for constructing a robust coating to replace the traditional modification without affecting the fiber intrinsic strength is an improved design and provides a new idea for the development of high-performance composites.

Polycrystalline Few-Layer Graphene as a Durable Anticorrosion Film for Copper.

Corrosion of metals in atmospheric environments is a worldwide problem in industry and daily life. Traditional anticorrosion methods including sacrificial anodes or protective coatings have performance limitations. Here, we report atomically thin, polycrystalline few-layer graphene (FLG) grown by chemical vapor deposition as a long-term protective coating film for copper (Cu). A six-year old, FLG-protected Cu is visually shiny and detailed material characterizations capture no sign of oxidation. The success of the durable anticorrosion film depends on the misalignment of grain boundaries between adjacent graphene layers. Theoretical calculations further found that corrosive molecules always encounter extremely high energy barrier when diffusing through the FLG layers. Therefore, the FLG is able to prevent the corrosive molecules from reaching the underlying Cu surface. This work highlights the interesting structures of polycrystalline FLG and sheds insight into the atomically thin coatings for various applications.

Tuning the Ratio of Pt(0)/Pt(II) in Well-Defined Pt Clusters Enables Enhanced Electrocatalytic Reduction/Oxidation of Hydrogen Peroxide for Sensitive Biosensing.

Rational design and construction of advanced sensing platforms for sensitive detection of H2O2 released from living cells is one of the challenges in the field of physiology and pathology. Noble metal clusters are a kind of nanomaterials with well-defined chemical composition and special atomic structures, which have been widely explored in catalysis, biosensing, and therapy. Compared with noble metal nanoparticles, noble metal clusters exhibit great potential in electrochemical biosensing due to their high atom utilization efficiency and abundant reactive active sites. Herein, Pt nanoclusters anchored on hollow carbon spheres (PtNCS/HCS) were successfully prepared for sensitive detection of H2O2. By tuning the ratio of Pt(0)/Pt(II) at different annealing temperatures, the optimized PtNCS/HCS-550 showed higher H2O2 reduction and oxidation catalytic activities than other control samples. Density functional theory calculations revealed that H2O2*can be better activated and dissociated in the Pt0II model featured with the co-existence of Pt(0)/Pt(II) and the key intermediates OOH*/OH* have a stronger interaction with the Pt0II model. As a concept application, the electrochemical biosensing platform was successfully applied to sensitive detection of H2O2 released from the cells.

Fe3C-Assisted Single Atomic Fe Sites for Sensitive Electrochemical Biosensing.

The rational construction of advanced sensing platforms to sensitively detect H2O2 produced by living cells is one of the challenges in both physiological and pathological fields. Owing to the extraordinary catalytic performances and similar metal coordination to natural metalloenzymes, single atomic site catalysts (SASCs) with intrinsic peroxidase (POD)-like activity have shown great promise for H2O2 detection. However, there still exists an obvious gap between them and natural enzymes because of the great challenge in rationally modulating the electronic and geometrical structures of central atoms. Note that the deliberate modulation of the metal-support interaction may give rise to the promising catalytic activity. In this work, an extremely sensitive electrochemical H2O2 biosensor based on single atomic Fe sites coupled with carbon-encapsulated Fe3C crystals (Fe3C@C/Fe-N-C) is proposed. Compared with the conventional Fe SASCs (Fe-N-C), Fe3C@C/Fe-N-C exhibits superior POD-like activity and electrochemical H2O2 sensing performance with a high sensitivity of 1225 µA/mM·cm2, fast response within 2 s, and a low detection limit of 0.26 µM. Significantly, sensitive monitoring of H2O2 released from living cells is also achieved. Moreover, the density functional theory calculations reveal that the incorporated Fe3C nanocrystals donate electrons to single atomic Fe sites, endowing them with improved activation ability of H2O2 and further enhancing the overall activity. This work provides a new design of synergistically enhanced single atomic sites for electrochemical sensing applications.

mTOR regulates GPVI-mediated platelet activation.

BACKGROUND: Due to mTOR (mammalian/mechanistic target of rapamycin) gene-loss mice die during embryonic development, the role of mTOR in platelets has not been evaluated using gene knockout technology. METHODS: A mouse model with megakaryocyte/platelet-specific deletion of mTOR was established, and be used to evaluate the role of mTOR in platelet activation and thrombus formation. RESULTS: mTOR-/- platelets were deficient in thrombus formation when grown on low-concentration collagen-coated surfaces; however, no deficiency in thrombus formation was observed when mTOR-/- platelets were perfused on higher concentration collagen-coated surfaces. In FeCl3-induced mouse mesenteric arteriole thrombosis models, wild-type (WT) and mTOR-/- mice displayed significantly different responses to low-extent injury with respect to the ratio of occluded mice, especially within the first 40 min. Additionally, mTOR-/- platelets displayed reduced aggregation and dense granule secretion (ATP release) in response to low doses of the glycoprotein VI (GPVI) agonist collagen related peptide (CRP) and the protease-activated receptor-4 (PAR4) agonist GYPGKF-NH2; these deficiencies were overcame by stimulation with higher concentration agonists, suggesting dose dependence of the response. At low doses of GPVI or PAR agonist, the activation of αIIbß3 in mTOR-/- platelets was reduced. Moreover, stimulation of mTOR-/- platelets with low-dose CRP attenuated the phosphorylation of S6K1, S6 and Akt Ser473, and increased the phosphorylation of PKCδ Thr505 and PKCε Ser729. Using isoform-specific inhibitors of PKCs (δ, ɛ, and α/ß), we established that PKCδ/ɛ, and especially PKCδ but not PKCα/ß or PKCθ, may be involved in low-dose GPVI-mediated/mTOR-dependent signaling. CONCLUSION: These observations indicate that mTOR plays an important role in GPVI-dependent platelet activation and thrombus formation.

The interferon stimulated gene 20 protein (ISG20) is an innate defense antiviral factor that discriminates self versus non-self translation.

ISG20 is a broad spectrum antiviral protein thought to directly degrade viral RNA. However, this mechanism of inhibition remains controversial. Using the Vesicular Stomatitis Virus (VSV) as a model RNA virus, we show here that ISG20 interferes with viral replication by decreasing protein synthesis in the absence of RNA degradation. Importantly, we demonstrate that ISG20 exerts a translational control over a large panel of non-self RNA substrates including those originating from transfected DNA, while sparing endogenous transcripts. This activity correlates with the protein's ability to localize in cytoplasmic processing bodies. Finally, these functions are conserved in the ISG20 murine ortholog, whose genetic ablation results in mice with increased susceptibility to viral infection. Overall, our results posit ISG20 as an important defense factor able to discriminate the self/non-self origins of the RNA through translation modulation.

LncRNA CBR3-AS1 potentiates Wnt/ß-catenin signaling to regulate lung adenocarcinoma cells proliferation, migration and invasion.

BACKGROUND: Long non-coding RNAs (lncRNAs) are pervasively transcribed in genome and emerging as a new player in tumorigenesis due to their functions in transcriptional, posttranscriptional and epigenetic mechanisms of gene regulation. As the most frequent malignancy and the foremost source of cancer mortality, lung cancer is a heterogeneous disorder. The most common type of lung cancer is Non-small cell lung cancer (NSCLC), occupying 85% of the total cases, and the main subtypes of NSCLC include lung adenocarcinoma (LAD), large cell carcinoma (LCC), and lung squamous cell carcinoma (LSCC). Recently, numerous lncRNAs have been reported to be strongly linked to NSCLC. In the present study, we found that a new lncRNA CBR3-AS1 is highly expressed in lung cancer. In addition, we also examined the expression of lncRNA CBR3-AS1 in 60 of LADs, 40 of LCCs and 40 of LSCCs patient samples, finding that CBR3-AS1 was specificity highly expressed in LAD cancer tissues. Mechanically, we discovered that CBR3-AS1 could regulate the proliferation, migration and invasion of LAD cells through targeting Wnt/ß-catenin signaling. METHODS: Real-time PCR, RNA-pulldown, RIP, western blotting, lentivirus transfection, luciferase reporter assays, cell proliferation assays, colony formation assays, wound healing scratch assays and transwell assays were employed to examine the relationship between lncRNA CBR3-AS1 and its regulation of Wnt/ß-catenin signaling in LAD cells. RESULTS: LncRNA CBR3-AS1 is highly-expressed in LAD and cell lines. LncRNA CBR3-AS1 shows physical association with ß-catenin. CBR3-AS1 could facilitate Wnt/ß-catenin signaling activation thought promoting nuclear localization of ß-catenin. CBR3-AS1 promotes LAD cell proliferation, migration and invasion by targeting Wnt/ß-catenin signaling. CONCLUSION: It can be found that a new functional lncRNA CBR3-AS1 could promote nuclear localization of ß-catenin so as to facilitate Wnt/ß-catenin signaling activation and regulate the proliferation, migration and invasion of LAD cells.

Health risk and temporal trend of dietary potentially toxic elements exposure in the residents of the Shenzhen metropolis, China, between 2005 and 2017: a risk assessment based on probabilistic estimation.

Dietary potentially toxic elements (PTEs) exposure in developing countries is of great concern. Probabilistic estimation exhibits great superiority in risk assessment by dealing with the variability and uncertainty of the parameters. Here, a probabilistic estimation based on two dimensions, PTEs in foods and food intake, was conducted. A total of 13 foods were collected from Shenzhen markets during 2005-2017, and the concentrations of Pb, Cd, Hg, and As were detected. A total of 853 residents from 245 households participated in a total diet study. The mean concentrations of Pb, Cd, Hg and As were 0.046, 0.0196, 0.0038, and 0.029 mg kg-1 in cereals, 0.042, 0.0174, 0.0027, and 0.014 mg kg-1 in vegetables, 0.044, 0.0237, 0.0056, and 0.021 mg kg-1 in meat, and 0.081, 0.1035, 0.0257, and 0.680 mg kg-1 in aquatic products, respectively. The probability density function showed that the 95th percentiles of the Pb, Cd, Hg, As hazard quotients (HQ) and the hazard index (HI) were 0.68, 1.57, 0.38, 5.81 and 7.51, respectively. Cumulative probability and sensitivity analysis showed that cereals and vegetables contributed most to Pb and Cd exposure; aquatic products to Hg exposure; and cereals and aquatic products to As exposure. The results showed that Shenzhen residents were at risk of exposure to Cd, As, and four PTEs in combination, although a temporal decreasing trend was observed. The probabilistic estimation used here reveals a complete picture of multiple PTEs exposure risk and identifies major contributing food categories, providing a valuable means for risk assessment.

Integrated transcriptomics and metabolomics analysis of catechins, caffeine and theanine biosynthesis in tea plant (Camellia sinensis) over the course of seasons.

BACKGROUND: Catechins, caffeine, and theanine as three important metabolites in the tea leaves play essential roles in the formation of specific taste and shows potential health benefits to humans. However, the knowledge on the dynamic changes of these metabolites content over seasons, as well as the candidate regulatory factors, remains largely undetermined. RESULTS: An integrated transcriptomic and metabolomic approach was used to analyze the dynamic changes of three mainly metabolites including catechins, caffeine, and theanine, and to explore the potential influencing factors associated with these dynamic changes over the course of seasons. We found that the catechins abundance was higher in Summer than that in Spring and Autumn, and the theanine abundance was significantly higher in Spring than that in Summer and Autumn, whereas caffeine exhibited no significant changes over three seasons. Transcriptomics analysis suggested that genes in photosynthesis pathway were significantly down-regulated which might in linkage to the formation of different phenotypes and metabolites content in the tea leaves of varied seasons. Fifty-six copies of nine genes in catechins biosynthesis, 30 copies of 10 genes in caffeine biosynthesis, and 12 copies of six genes in theanine biosynthesis were detected. The correlative analysis further presented that eight genes can be regulated by transcription factors, and highly correlated with the changes of metabolites abundance in tea-leaves. CONCLUSION: Sunshine intensity as a key factor can affect photosynthesis of tea plants, further affect the expression of major Transcription factors (TFs) and structural genes in, and finally resulted in the various amounts of catechins, caffeine and theaine in tea-leaves over three seasons. These findings provide new insights into abundance and influencing factors of metabolites of tea in different seasons, and further our understanding in the formation of flavor, nutrition and medicinal function.

Discovery of a novel selective water-soluble SMAD3 inhibitor as an antitumor agent.

Targeting the SMAD3 protein is an attractive therapeutic strategy for treating cancer, as it avoids the potential toxicities due to targeting the TGF-ß signaling pathway upstream. Compound SIS3 was the first selective SMAD3 inhibitor developed that had acceptable activity, but its poor water solubility limited its development. Here, a series of SIS3 analogs was created to investigate the structure-activity relationship for inhibiting the activation of SMAD3. On the basis of this SAR, further optimization generated a water-soluble compound, 16d, which was capable of effectively blocking SMAD3 activation in vitro and had similar NK cell-mediated anticancer effects in vivo to its parent SIS3. This study not only provided a preferable lead compound, 16d, for further drug discovery or a potential tool to study SMAD3 biology, but also proved the effectiveness of our strategy for water-solubility driven optimization.

Synthesis and biological evaluation of parthenolide derivatives with reduced toxicity as potential inhibitors of the NLRP3 inflammasome.

Parthenolide (PTL) can target NLRP3 inflammasome to treat inflammation and its related disease, but its cytotoxicity limits further development as an anti-inflammatory drug. A series of PTL analogs and their Michael-type adducts were designed and synthesized, and most of them showed high activities against the NLRP3 inflammasome pathway. The most potent compound 8b inhibited the release of IL-1ß with IC50 values of 0.3 µM in J774A.1 cell and 1.0 µM in primary glial cells, respectively. Moreover, 8b showed low toxicity against J774A.1 cell (IC50 = 24.1 µM) and HEK-293T (IC50 = 69.8 µM) with a ~8 folds increase of therapeutic index compared to its parent PTL. The preliminary mechanism study revealed that 8b mediated anti-inflammation is associated with the NLRP3 inflammasome signal pathway. Based on these investigations, we propose that 8b might be a potential drug candidate for ultimate development of the anti-inflammation drug.

The characteristics and genome analysis of vB_ApiP_XC38, a novel phage infecting Acinetobacter pittii.

Acinetobacter pittii is an important pathogen causing nosocomial infection worldwide. In this study, a multidrug-resistant A. pittii ABC38 was used as host bacterium to isolate the lytic phage vB_ApiP_XC38. The biological characteristics of vB_ApiP_XC38 were studied and the genome was sequenced and analyzed. vB_ApiP_XC38 belonged to Podoviridae family. The phage had double-stranded genome, which comprised 79,328 bp with 39.58% G+C content displaying very low similarity (< 1% identity) with published genomes of other phages and bacteria. A total of 97 open reading frames (ORFs) were predicted and contained nucleotide metabolism and replication module, structural components module, and lysis module. The ANI, AAI, and phylogenetic analysis indicated that all phages were found distant from vB_ApiP_XC38. Altogether, morphological, genomics, and phylogenetic analysis suggest that vB_ApiP_XC38 is more likely a novel phage of A. pittii.