Phosphoproteomic analysis reveals changes in A-Raf-related protein phosphorylation in response to Toxoplasma gondii infection in porcine macrophages.

BACKGROUND: Toxoplasma gondii is an obligate intracellular protozoan parasite that causes severe threats to humans and livestock. Macrophages are the cell type preferentially infected by T. gondii in vivo. Protein phosphorylation is an important posttranslational modification involved in diverse cellular functions. A rapidly accelerated fibrosarcoma kinase (A-Raf) is a member of the Raf family of serine/threonine protein kinases that is necessary for MAPK activation. Our previous research found that knockout of A-Raf could reduce T. gondii-induced apoptosis in porcine alveolar macrophages (3D4/21 cells). However, limited information is available on protein phosphorylation variations and the role of A-Raf in macrophages infected with T. gondii. METHODS: We used immobilized metal affinity chromatography (IMAC) in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS) to profile changes in phosphorylation in T. gondii-infected 3D4/21 and 3D4/21-ΔAraf cells. RESULTS: A total of 1647 differentially expressed phosphorylated proteins (DEPPs) with 3876 differentially phosphorylated sites (DPSs) were identified in T. gondii-infected 3D4/21 cells (p3T group) when compared with uninfected 3D4/21 cells (pho3 group), and 959 DEPPs with 1540 DPSs were identified in the p3T group compared with infected 3D4/21-ΔAraf cells (p3KT group). Venn analysis revealed 552 DPSs corresponding to 406 DEPPs with the same phosphorylated sites when comparing p3T/pho3 versus p3T/p3KT, which were identified as DPSs and DEPPs that were directly or indirectly related to A-Raf. CONCLUSIONS: Our results revealed distinct responses of macrophages to T. gondii infection and the potential roles of A-Raf in fighting infection via phosphorylation of crucial proteins.

Comprehensive mapping of saliva by multiomics in children with idiopathic nephrotic syndrome.

AIM: Saliva can reflect an individual's physiological status or susceptibility to systemic disease. However, little attention has been given to salivary analysis in children with idiopathic nephrotic syndrome (INS). We aimed to perform a comprehensive analysis of saliva from INS children. METHODS: A total of 18 children (9 children with INS and 9 normal controls) were recruited. Saliva was collected from each INS patient in the acute and remission phases. 16S rRNA gene sequencing, widely targeted metabolomics, and 4D-DIA proteomics were performed. RESULTS: Actinobacteria and Firmicutes were significantly enriched in the pretreatment group compared with the normal control group, while Bacteroidota and Proteobacteria were significantly decreased. A total of 146 metabolites were identified as significantly different between INS children before treatment and normal controls, which covers 17 of 23 categories. KEGG enrichment analysis revealed three significantly enriched pathways, including ascorbate and aldarate metabolism, pentose and glucuronate interconversions, and terpenoid backbone biosynthesis (P < 0.05). A total of 389 differentially expressed proteins were selected between INS children before treatment and normal controls. According to the KEGG and GO enrichment analyses of the KOGs, abnormal ribosome structure and function and humoral immune disorders were the most prominent differences between INS patients and normal controls in the proteomic analysis. CONCLUSION: Oral microbiota dysbiosis may modulate the metabolic profile of saliva in children with INS. It is hypothesized that children with INS might have "abnormal ribosome structure and function" and "humoral immune disorders".

Theoretical and Experimental Aspects of Electrocatalysts for Oxygen Evolution Reaction.

Scientists are increasingly paying attention to using theoretical design as a guide combined with modern in-situ characterization techniques to develop catalysts with high activity, low cost, and long-term life. The review discusses the progress of catalyst theoretical design and corresponding experiments based on three typical oxygen evolution catalytic mechanisms, including the adsorbate evolution, lattice oxygen-mediated, and unconventional bifunctional mechanisms. This work briefly describes the commonly used tools and descriptors in theory as well as the electrochemical techniques and characterizations in experiments. Our purpose is to sort out the ways to closely integrate the theoretical method and experimental verification from the perspective of reaction mechanism, and to provide some experience reference for the future development of theoretical tools and experimental technologies.

Toxoplasma gondii infection regulates apoptosis of host cells via miR-185/ARAF axis.

BACKGROUND: Toxoplasmosis is a zoonosis with a worldwide presence that is caused by the intracellular parasite Toxoplasma gondii. Active regulation of apoptosis is an important immune mechanism by which host cells resist the growth of T. gondii or avoid excessive pathological damage induced by this parasite. Previous studies found that upregulated expression of microRNA-185 (miR-185) during T. gondii infection has a potential role in regulating the expression of the ARAF gene, which is reported to be associated with cell proliferation and apoptosis. METHODS: The expression levels of miR-185 and the ARAF gene were evaluated by qPCR and Western blot, respectively, in mice tissues, porcine kidney epithelial cells (PK-15) and porcine alveolar macrophages (3D4/21) following infection with the T. gondii ToxoDB#9 and RH strains. The dual luciferase reporter assay was then used to verify the relationship between miR-185 and ARAF targets in PK-15 cells. PK-15 and 3D4/21 cell lines with stable knockout of the ARAF gene were established by CRISPR, and then the apoptosis rates of the cells following T. gondii infection were detected using cell flow cytometry assays. Simultaneously, the activities of cleaved caspase-3, as a key apoptosis executive protein, were detected by Western blot to evaluate the apoptosis levels of cells. RESULTS: Infection with both the T. gondii ToxoDB#9 and RH strains induced an increased expression of miR-185 and a decreased expression of ARAF in mice tissues, PK-15 and 3D4/21 cells. MiR-185 mimic transfections showed a significantly negative correlation in expression levels between miR-185 and the ARAF gene. The dual luciferase reporter assay confirmed that ARAF was a target of miR-185. Functional investigation revealed that T. gondii infection induced the apoptosis of PK-15 and 3D4/21 cells, which could be inhibited by ARAF knockout or overexpression of miR-185. The expression levels of cleaved caspase-3 protein were significantly lower in cells with ARAF knockout than in normal cells, which were consistent with the results of the cell flow cytometry assays. CONCLUSIONS: Toxoplasma gondii infection could lead to the upregulation of miR-185 and the downregulation of ARAF, which was not related to the strain of T. gondii and the host cells. Toxoplasma gondii infection could regulate the apoptosis of host cells via the miR-185/ARAF axis, which represents an additional strategy used by T. gondii to counteract host-cell apoptosis in order to maintain survival and reproduce in the host cells.

NiS gradient distribution on arrayed porous carbonized grapefruit peel for water splitting.

Metal-based catalysts on biomass carbon substrates can combine their respective advantages of composition and structure to improve the catalytic performance. Herein, NiS supported on grapefruit peel derived array porous carbon (APC) was obtained via a carbonization process without emission of toxic gases. The natural S source from grapefruit peel reacted with nickel salt solution. The gradient distribution of NiS and S on the APC substrates can be altered by the concentration of impregnating salt solution. Theoretical calculations showed that the S gradient distribution on APC could tune the electronic structure and optimize the adsorption energies of the intermediates. NiS was firmly anchored on the porous carbon framework, resulting in enhanced high intrinsic activity, exposure of more active sites, and accelerated mass transfer. The active mass density was proposed to build a relationship between active metal content and electrolyte diffusion capacity for the evaluation of catalytic properties.

Effect of Intrinsic Pore Distribution on Ion Diffusion Kinetics of Supercapacitor Electrode Surface.

The electrolyte ion diffusion kinetics have an important impact on electrochemical energy storage. Herein, we report the effect of the intrinsic porosity of NiCoP on accelerating electrolyte ion diffusion kinetics and accommodating volume expansion during the charge/discharge process. The pore distribution model of electrode/electrolyte was designed and optimized by the finite element simulation, demonstrating the visualization and quantitative analysis of the diffusion process of the electrode/electrolyte interface with intrinsic porous structure. When the pore area ratio reached 50.01%, the theoretical diffusion coefficient of 1.41 × 10-11 m2 s-1 would be conducive to the rapid diffusion of electrolytes. The electrode gained a specific capacity of 2805 F g-1 at a current density of 1 A g-1 based on the measured diffusion coefficient (1.79 × 10-10 m2 s-1), superior to 1.44-times that of the pristine electrode. The diffusion barriers of intrinsic porous NiCoP (3.19 eV) and conventional NiCoP (47.10 eV) were calculated by the density functional theory calculations, respectively. The intrinsic porous NiCoP was prepared by the hydrothermal treatment, annealing, and phosphating processes. The pore distribution was regulated by the concentration of NaHCO3 as a pore-forming additive. This work combines simulations and experiments to form a method to optimize diffusion kinetics at the electrode/electrolyte interface.

Rapid surface reconstruction strategies for oxygen evolution reactions: chemical grafting of MXene quantum dots on Ni-Co layered double hydroxides.

The surface reconstruction of transition metal-based catalysts with their specific catalytic mechanism is currently one of the hotspots and difficulties in the electrocatalytic oxygen evolution reaction (OER). Herein, a chemical grafting strategy was proposed to facilitate the surface reconstruction of Ni-Co layered double hydroxide@MXene quantum dot (Ni-Co LDH@MQDs) electrocatalysts to optimize the OER kinetics. The surface reconstruction of Ni-Co LDH@MQDs was predicted and monitored by a combination of ab initio molecular dynamics, density functional theory and experimental verification. Compared with weak electrostatic bonds, the rapid surface evolution of electrocatalysts can be revealed due to the strong chemical grafting between the MQDs and LDHs. The reconstituted Ni-Co LDH@MQD electrocatalysts undergo an unconventional bifunctional mechanism to lower the barriers of the rate-limiting step of the OER. This work provides a research strategy for transition metal catalysts for efficient catalysis by designing surface reconfiguration.

Comparison of different algorithms based on TKEO for EMG change point detection.

Objective.A significant challenge in surface electromyography (EMG) is the accurate identification of onset and offset of muscle activation while maintaining high real-time performance. Teager-Kaiser energy operator (TKEO) is widely used in muscle activity monitoring systems because of its computational simplicity and strong real-time performance. However, in contrast to TKEO ontology, few studies have examined how well the energy operator variants from multiple fields perform in conditioning EMG signals. This paper aims to investigate the role of the energy operator and its variants in EMG change point detection by a threshold detector.Approach.To compare the stability and accuracy of TKEO and its variants for EMG change point detection, the EMG data of extensor carpi radialis longus and flexor carpi radialis were acquired from twenty participants operating a controller under normal and disturbed conditions, and EMG change point detection was performed by four energy operators and their rectified versions.Main results.Based on the 'standard' change points collected by the controller, the detection results were evaluated by three evaluation indexes: detection rate,F1 Score, and accuracy. The experimental results show that the multiresolution energy operator and the TKEO with rectified (abs-TKEO) are more suitable for EMG change point detection.Significance.This paper compared the effect of the energy operator and its variants on a threshold-based EMG change point detector. The experimental results in this paper can provide a reference for the selection of EMG signal conditioning methods to improve the detection performance of the EMG change point detector.

Cluster analysis of splenocyte microRNAs in the pig reveals key signal regulators of immunomodulation in the host during acute and chronic Toxoplasma gondii infection.

BACKGROUND: Toxoplasma gondii is an obligate intracellular protozoan parasite that can cause a geographically widespread zoonosis. Our previous splenocyte microRNA profile analyses of pig infected with T. gondii revealed that the coordination of a large number of miRNAs regulates the host immune response during infection. However, the functions of other miRNAs involved in the immune regulation during T. gondii infection are not yet known. METHODS: Clustering analysis was performed by K-means, self-organizing map (SOM), and hierarchical clustering to obtain miRNA groups with the similar expression patterns. Then, the target genes of the miRNA group in each subcluster were further analyzed for functional enrichment by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome pathway to recognize the key signaling molecules and the regulatory signatures of the innate and adaptive immune responses of the host during T. gondii infection. RESULTS: A total of 252 miRNAs were successfully divided into 22 subclusters by K-means clustering (designated as K1-K22), 29 subclusters by SOM clustering (designated as SOM1-SOM29), and six subclusters by hierarchical clustering (designated as H1-H6) based on their dynamic expression levels in the different infection stages. A total of 634, 660, and 477 GO terms, 15, 26, and 14 KEGG pathways, and 16, 15, and 7 Reactome pathways were significantly enriched by K-means, SOM, and hierarchical clustering, respectively. Of note, up to 22 miRNAs mainly showing downregulated expression at 50 days post-infection (dpi) were grouped into one subcluster (namely subcluster H3-K17-SOM1) through the three algorithms. Functional analysis revealed that a large group of immunomodulatory signaling molecules were controlled by the different miRNA groups to regulate multiple immune processes, for instance, IL-1-mediated cellular response and Th1/Th2 cell differentiation partly depending on Notch signaling transduction for subclusters K1 and K2, innate immune response involved in neutrophil degranulation and TLR4 cascade signaling for subcluster K15, B cell activation for subclusters SOM17, SOM1, and SOM25, leukocyte migration, and chemokine activity for subcluster SOM9, cytokine-cytokine receptor interaction for subcluster H2, and interleukin production, chemotaxis of immune cells, chemokine signaling pathway, and C-type lectin receptor signaling pathway for subcluster H3-K17-SOM1. CONCLUSIONS: Cluster analysis of splenocyte microRNAs in the pig revealed key regulatory properties of subcluster miRNA molecules and important features in the immune regulation induced by acute and chronic T. gondii infection. These results contribute new insight into the identification of physiological immune responses and maintenance of tolerance in pig spleen tissues during T. gondii infection.

Industry 4.0 Engineering Product Life Cycle Management Based on Multigranularity Access Control Model.

In order to improve the management efficiency of the safety status of Industry 4.0 engineering products, the multigranularity access control model (MGACM) Industry 4.0 engineering product life cycle management (PLM) is adopted to optimize the safety management mode of Industry 4.0 engineering products in this paper. The multigranularity access control model is constructed in this paper, which has strong nonlinearity and better fault tolerance. In addition, the parameters of PLM are optimized through the multiparticle access control model, and PLM search is enabled. Taking into account the slow and easy convergence of the multigranular access control model, a niche technology with full life cycle heterogeneity and elimination mechanism is proposed to solve the premature convergence problem of the multigranular access control model. The final simulation results of this paper show that, compared with traditional algorithms, the proposed multigranularity access control model is more reliable and effective and has faster convergence speed and higher management efficiency.