Comprehensive analysis of the relationship between ubiquitin-specific protease 21 (USP21) and prognosis, tumor microenvironment infiltration, and therapy response in colorectal cancer.

BACKGROUND: Ubiquitin-specific proteases family is crucial to host immunity against pathogens. However, the correlations between USP21 and immunosurveillance and immunotherapy for colorectal cancer (CRC) have not been reported. METHODS: The differential expression of USP21 between CRC tissues and normal tissues was analyzed using multiple public databases. Validation was carried out in clinical samples through qRT-PCR and IHC. The correlation between USP21 and the prognosis, as well as clinical pathological characteristics of CRC patients, was investigated. Moreover, cell models were established to assess the influence of USP21 on CRC growth and progression, employing CCK-8 assays, colony formation assays, and wound-healing assays. Subsequently, gene set variation analysis (GSVA) was used to explore the potential biological functions of USP21 in CRC. The study also examined the impact of USP21 on cytokine levels and immune cell infiltration in the tumor microenvironment (TME). Finally, the effect of USP21 on the response to immunotherapy and chemotherapy in CRC was analyzed. RESULTS: The expression of USP21 was significantly upregulated in CRC. High USP21 is correlated with poor prognosis in CRC patients and facilitates the proliferation and migration capacities of CRC cells. GSVA indicated an association between low USP21 and immune activation. Moreover, low USP21 was linked to an immune-activated TME, characterized by high immune cell infiltration. Importantly, CRC with low USP21 exhibited higher tumor mutational burden, high PD-L1 expression, and better responsiveness to immunotherapy and chemotherapeutic drugs. CONCLUSION: This study revealed the role of USP21 in TME, response to therapy, and clinical prognosis in CRC, which provided novel insights for the therapeutic application in CRC.

Artificial Intelligence-Enhanced Waveguide "Photonic Nose"- Augmented Sensing Platform for VOC Gases in Mid-Infrared.

On-chip nanophotonic waveguide sensor is a promising solution for miniaturization and label-free detection of gas mixtures utilizing the absorption fingerprints in the mid-infrared (MIR) region. However, the quantitative detection and analysis of organic gas mixtures is still challenging and less reported due to the overlapping of the absorption spectrum. Here,an Artificial-Intelligence (AI) assisted waveguide "Photonic nose" is presented as an augmented sensing platform for gas mixture analysis in MIR. With the subwavelength grating cladding supported waveguide design and the help of machine learning algorithms, the MIR absorption spectrum of the binary organic gas mixture is distinguished from arbitrary mixing ratio and decomposed to the single-component spectra for concentration prediction. As a result, the classification of 93.57% for 19 mixing ratios is realized. In addition, the gas mixture spectrum decomposition and concentration prediction show an average root-mean-square error of 2.44 vol%. The work proves the potential for broader sensing and analytical capabilities of the MIR waveguide platform for multiple organic gas components toward MIR on-chip spectroscopy.

Pro-phagocytic function and structural basis of GPR84 signaling.

GPR84 is a unique orphan G protein-coupled receptor (GPCR) that can be activated by endogenous medium-chain fatty acids (MCFAs). The signaling of GPR84 is largely pro-inflammatory, which can augment inflammatory response, and GPR84 also functions as a pro-phagocytic receptor to enhance phagocytic activities of macrophages. In this study, we show that the activation of GPR84 by the synthetic agonist 6-OAU can synergize with the blockade of CD47 on cancer cells to induce phagocytosis of cancer cells by macrophages. We also determine a high-resolution structure of the GPR84-Gi signaling complex with 6-OAU. This structure reveals an occluded binding pocket for 6-OAU, the molecular basis of receptor activation involving non-conserved structural motifs of GPR84, and an unusual Gi-coupling interface. Together with computational docking and simulations studies, this structure also suggests a mechanism for the high selectivity of GPR84 for MCFAs and a potential routes of ligand binding and dissociation. These results provide a framework for understanding GPR84 signaling and developing new drugs targeting GPR84.

A new Mn-based layered cathode with enlarged interlayer spacing for potassium ion batteries.

Layered Mn-based cathode (KxMnO2) has attracted wide attention for potassium ion batteries (PIBs) because of its high specific capacity and energy density. However, the structure and capacity of KxMnO2 cathode are constantly degraded during the cycling due to the strong Jahn-Teller effect of Mn3+ and huge ionic radius of K+. In this work, lithium ion and interlayer water were introduced into Mn layer and K layer in order to suppress the Jahn-Teller effect and expand interlayer spacing, respectively, thus obtaining new types of K0.4Mn1-xLixO2·0.33H2O cathode materials. The interlayer spacing of the K0.4MnO2 increased from 6.34 to 6.93 Å after the interlayer water insertion. X-ray photoelectron spectroscopy studies demonstrated that proper lithium doping can effectively control the ratio of Mn3+/Mn4+ and inhibit the Jahn-Teller effect. In-situ X-ray diffraction exhibited that lithium doping can inhibit the irreversible phase transition and improve the structural stability of materials during cycling. As a result, the optimal K0.4Mn0.9Li0.1O2·0.33H2O not only delivered a higher capacity retention of 84.04 % compared to the value of 28.09 % for K0.4MnO2·0.33H2O, but also maintained a greatly enhanced rate capability. This study provides a new opportunity for designing layered manganese-based cathode materials with high performance for PIBs.

Expanding chiral metamaterials for retrieving fingerprints via vibrational circular dichroism.

Circular dichroism (CD) spectroscopy has been widely demonstrated for detecting chiral molecules. However, the determination of chiral mixtures with various concentrations and enantiomeric ratios can be a challenging task. To solve this problem, we report an enhanced vibrational circular dichroism (VCD) sensing platform based on plasmonic chiral metamaterials, which presents a 6-magnitude signal enhancement with a selectivity of chiral molecules. Guided by coupled-mode theory, we leverage both in-plane and out-of-plane symmetry-breaking structures for chiral metamaterial design enabled by a two-step lithography process, which increases the near-field coupling strengths and varies the ratio between absorption and radiation loss, resulting in improved chiral light-matter interaction and enhanced molecular VCD signals. Besides, we demonstrate the thin-film sensing process of BSA and ß-lactoglobulin proteins, which contain secondary structures α-helix and ß-sheet and achieve a limit of detection down to zeptomole level. Furthermore, we also, for the first time, explore the potential of enhanced VCD spectroscopy by demonstrating a selective sensing process of chiral mixtures, where the mixing ratio can be successfully differentiated with our proposed chiral metamaterials. Our findings improve the sensing signal of molecules and expand the extractable information, paving the way toward label-free, compact, small-volume chiral molecule detection for stereochemical and clinical diagnosis applications.

Pro-phagocytic function and structural basis of GPR84 signaling.

GPR84 is a unique orphan G protein-coupled receptor (GPCR) that can be activated by endogenous medium-chain fatty acids (MCFAs). The signaling of GPR84 is largely pro-inflammatory, which can augment inflammatory response, and GPR84 also functions as a pro-phagocytic receptor to enhance the phagocytic activities of macrophages. In this study, we first showed that the activation of GPR84 by the synthetic agonist 6-OAU could synergize with the blockade of CD47 on cancer cells to induce phagocytosis of cancer cells by macrophages. Then, we determined a high-resolution structure of the GPR84-Gi signaling complex with 6-OAU. This structure revealed a completely occluded binding pocket for 6-OAU, the molecular basis of receptor activation involving non-conserved structural motifs of GPR84, and an unusual Gi-coupling interface. Together with computational docking and simulations studies, our structure also suggested the mechanism for the high selectivity of GPR84 for MCFAs and the potential routes of ligand binding and dissociation. Our results provide a framework for understanding GPR84 signaling and developing new drugs targeting GPR84.

Reaching the initial coulombic efficiency and structural stability limit of P2/O3 biphasic layered cathode for sodium-ion batteries.

The P2/O3 biphasic layered oxide (NaxMn1-yMyO2, M: doping elements) is a cathode family with great promise for sodium-ion batteries (SIBs) because of their tunable electrochemical performance and low cost. However, the ultrahigh initial coulombic efficiency (ICE) and inferior cycling performance of P2/O3-NaxMn1-yMyO2 need to be improved for practical application. Herein, Ni/Cu co-doped P2/O3-Na0.75Mn1-yNiy-zCuzO2 materials are well-designed. The ultrahigh ICE can be restrained by altering the ratio of P2/O3 via adjusting Ni content, and the structural stability can be improved by Cu doping via enlarging parameter c of O3 phase and suppressing irreversible P2-O2 phase transformation. The optimal P2/O3-Na0.75Mn0.6Ni0.3Cu0.1O2 delivers a capacity of 142.4 with ICE of 107.8%, superior capacity retention in the temperature range of -40 âˆ¼ 30 °C, and rate performance of 95.9 mAh g-1 at 1.2 A g-1. The overall storage mechanism of P2/O3-Na0.75Mn0.6Ni0.3Cu0.1O2 is revealed by the combination of electrochemical profiles, in situ X-ray diffraction, and first-principles calculations. The Na-ion full battery based on P2/O3-Na0.75Mn0.6Ni0.3Cu0.1O2 cathode can achieve a remarkable energy density of 306.9 Wh kg-1 with a power density of 695.5 W kg-1 at 200 mA g-1. This work may shed light on the rational design of high-performance P2/O3 biphasic layered cathode for SIBs.

Midinfrared Spectroscopic Analysis of Aqueous Mixtures Using Artificial-Intelligence-Enhanced Metamaterial Waveguide Sensing Platform.

As miniaturized solutions, mid-infrared (MIR) waveguide sensors are promising for label-free compositional detection of mixtures leveraging plentiful absorption fingerprints. However, the quantitative analysis of liquid mixtures is still challenging using MIR waveguide sensors, as the absorption spectrum overlaps for multiple organic components accompanied by strong water absorption background. Here, we present an artificial-intelligence-enhanced metamaterial waveguide sensing platform (AIMWSP) for aqueous mixture analysis in the MIR. With the sensitivity-improved metamaterial waveguide and assistance of machine learning, the MIR absorption spectra of a ternary mixture in water can be successfully distinguished and decomposed to single-component spectra for predicting concentration. A classification accuracy of 98.88% for 64 mixing ratios and 92.86% for four concentrations below the limit of detection (972 ppm, based on 3σ) with steps of 300 ppm are realized. Besides, the mixture concentration prediction with root-mean-squared error varying from 0.107 vol % to 1.436 vol % is also achieved. Our work indicates the potential of further extending this sensing platform to MIR spectrometer-on-chip aiming for the data analytics of multiple organic components in aqueous environments.

Hubbing the Cancer Cell.

Oncogenic transformation drives adaptive changes in a growing tumor that affect the cellular organization of cancerous cells, resulting in the loss of specialized cellular functions in the polarized compartmentalization of cells. The resulting altered metabolic and morphological patterns are used clinically as diagnostic markers. This review recapitulates the known functions of actin, microtubules and the γ-tubulin meshwork in orchestrating cell metabolism and functional cellular asymmetry.

Larger-Than-Unity External Optical Field Confinement Enabled by Metamaterial-Assisted Comb Waveguide for Ultrasensitive Long-Wave Infrared Gas Spectroscopy.

Nanophotonic waveguides that implement long optical pathlengths on chips are promising to enable chip-scale gas sensors. Nevertheless, current absorption-based waveguide sensors suffer from weak interactions with analytes, limiting their adoptions in most demanding applications such as exhaled breath analysis and trace-gas monitoring. Here, we propose an all-dielectric metamaterial-assisted comb (ADMAC) waveguide to greatly boost the sensing capability. By leveraging large longitudinal electric field discontinuity at periodic high-index-contrast interfaces in the subwavelength grating metamaterial and its unique features in refractive index engineering, the ADMAC waveguide features strong field delocalization into the air, pushing the external optical field confinement factor up to 113% with low propagation loss. Our sensor operates in the important but underdeveloped long-wave infrared spectral region, where absorption fingerprints of plentiful chemical bonds are located. Acetone absorption spectroscopy is demonstrated using our sensor around 7.33 µm, showing a detection limit of 2.5 ppm with a waveguide length of only 10 mm.

Optimization of production of recombinant gamma-tubulin in bacteria.

Production of a protein of interest in bacteria and its purification from bacterial lysates are valuable tools for the purification of larger amounts of recombinant proteins. The low cost of culturing, and the rapid cell growth of bacteria make this host a good choice for protein production, but the folding and function of the purified protein might be altered due to the production of a eukaryotic protein in a prokaryotic host. Here, we provide a purification method for the purification of gamma (γ)-tubulin (TUBG) from soluble fractions of Escherichia (E.) coli lysates using affinity tags.•This protocol describes a method that purifies soluble GST-TUBG1 from bacteria.•Of the three tested induction conditions, the highest yield of recombinant GST-TUBG1 was obtained after the induction of E. coli with isopropyl-D-1-thiogalactopyranoside (IPTG) for 1 h at 37 °C followed by overnight incubation at room temperature.•In comparison with other methodologies (Hoog et al., 2011), the technique described here retrieves larger amounts of recombinant TUBG1 from small-scale expression cultures.

The γ-tubulin meshwork assists in the recruitment of PCNA to chromatin in mammalian cells.

Changes in the location of γ-tubulin ensure cell survival and preserve genome integrity. We investigated whether the nuclear accumulation of γ-tubulin facilitates the transport of proliferating cell nuclear antigen (PCNA) between the cytosolic and the nuclear compartment in mammalian cells. We found that the γ-tubulin meshwork assists in the recruitment of PCNA to chromatin. Also, decreased levels of γ-tubulin reduce the nuclear pool of PCNA. In addition, the γ-tubulin C terminus encodes a PCNA-interacting peptide (PIP) motif, and a γ-tubulin-PIP-mutant affects the nuclear accumulation of PCNA. In a cell-free system, PCNA and γ-tubulin formed a complex. In tumors, there is a significant positive correlation between TUBG1 and PCNA expression. Thus, we report a novel mechanism that constitutes the basis for tumor growth by which the γ-tubulin meshwork maintains indefinite proliferation by acting as an opportune scaffold for the transport of PCNA from the cytosol to the chromatin.

Mechanical Performance of Steel Slag Concrete under Biaxial Compression.

The mechanical performance of steel slag concrete (SSC) under biaxial compression is investigated by a servo-controlled static-dynamic true triaxial machine (TAWZ-5000/3000). Three replacement ratios of steel slags and four kinds of stress ratio (0.25:1, 0.5:1, 0.75:1, and 1:1) are examined in this study. According to the test results, the influences of replacement ratio and stress ratio on the strength, deformation properties, stress-strain curves, and failure mode of SSC are analyzed. The results show that the failure mode of SSC under biaxial compression is plate-splitting crack. Both the strength and deformation of SSC are larger than the corresponding values of the uniaxial compression. Under the same stress ratio, the value of principal stress σ 3 f increases first and then decreases with the increase in the replacement ratio. Under the same replacement ratio, σ 3 f increases first and then decreases as the stress ratio increases, and the maximum of σ 3 f is obtained at the stress ratio of α = 0.5:1. Based on the analysis and test data, the strength failure criterion of SSC under biaxial compression stresses is proposed.

Experimental Investigation on the Impact Resistance of Carbon Fibers Reinforced Coral Concrete.

In this study, the impact resistance of coral concrete with different carbon fiber (CF) dosages subjected to drop-weight impact test was investigated. For this purpose, three concrete strength grades (C20, C30, C40) and six CF dosages (0.0%, 0.3%, 0.6%, 1.0%, 1.5%, and 2.0% by weight of the binder) were considered, and a total of 18 groups of carbon fibers reinforced coral concrete (CFRCC) were cast. For each group, eight specimens were tested following the drop-weight impact test suggested by CECS 13. Then, the two-parameter Weibull distribution theory was adopted to statistically analyze the variations in experimental results. The results indicated that the addition of CFs could transform the failure pattern from obvious brittleness to relatively good ductility and improve the impact resistance of coral concrete. Moreover, the impact resistance of CFRCC increases with the CF dosage increasing. The statistical analysis showed that the probability distribution of the blow numbers at the initial crack and final failure of CFRCC approximately follows the two-parameter Weibull distribution.

UHPLC/QTOF-MS-based metabolomics reveal the effect of Melastoma dodecandrum extract in type 2 diabetic rats.

Context: Melastoma dodecandrum Lour. (Melastomataceae) is a traditional Chinese medicine. This is the first study to report a protective effect of the ethanol extract from M. dodecandrum (MDE) in type 2 diabetic (T2DM) rats.Objective: To investigate the therapeutic mechanism of MDE in T2DM rats.Materials and methods: Sprague-Dawley rats were fed a high-fat diet for 6 consecutive weeks, followed by intraperitoneal injection of streptozotocin (STZ) (30 mg/kg) to induce diabetes. T2DM rats were divided into untreated diabetic, metformin-treated and MDE-treated groups. Additionally, normal rats without treatment served as the control group (n = 6). Metformin (250 mg/kg) and MDE (600 mg/kg) were intragastrically administered to T2DM rats for 5 consecutive weeks. Serum samples were evaluated via ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC/QTOF-MS), followed by principal components analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA).Results: The 17 identified potential biomarkers were mainly involved in lipid, amino acid, arachidonic acid, taurine and nicotinic acid metabolism. MDE also significantly reduced the level of fasting blood glucose (FBG), oral glucose tolerance, insulin, total cholesterol (TC), triglyceride (TG), low-density lipoprotein (LDL), malondialdehyde (MDA), aspartate aminotransferase (AST), alanine aminotransferase (ALT) and urea nitrogen (BUN) in T2DM rats. The high-density lipoprotein (HDL), serum creatinine (Scr), superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) levels were elevated in MDE-treated group.Discussion and conclusion: MDE possesses substantial antidiabetic activity, especially in lipid disorder regulation. This suggests that the use of MDE can be generalized to broader pharmacological studies, such as obesity and hyperlipidaemia.

Association between the perturbation of bile acid homeostasis and valproic acid-induced hepatotoxicity.

Valproic acid (VPA), a widely prescribed antiepileptic drug, is known to induce hepatotoxicity. However, the mechanisms underlying this toxicity are not well understood. In this study, we performed a nontargeted metabolomic analysis of children with epilepsy treated with VPA (n = 23). Metabolic pathway analysis showed that the fatty acid pathway, citrate cycle, urea cycle, amino acid metabolism, and bile acid pathway were altered in children with epilepsy exhibiting VPA hepatotoxicity. In particular, the VPA-induced perturbation of bile acid homeostasis has not been observed previously. Based on these findings, we performed a targeted metabolomic analysis to characterize bile acid profiles and further determined the effects of VPA on the synthesis, transport, and regulation of bile acids in mice. The bile acid metabolomic profiles of the livers of mice treated with VPA indicated an increase in most bile acids, especially chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA), as well as unconjugated bile acids. The upregulation of genes related to bile acid synthesis (CYP7A1 and CYP8B1) and the downregulation of genes related to conjugation (BAAT and BACS) and regulation (FXR and SHP) were detected in the liver, suggesting that hydrophobic bile acid production was increased and FXR signaling was impaired. Our results suggest that the perturbation of bile acid homeostasis and impaired FXR signaling are involved in VPA-induced hepatotoxicity, providing a novel insight into VPA hepatotoxicity.

Cucurbitacin B suppresses proliferation of pancreatic cancer cells by ceRNA: Effect of miR-146b-5p and lncRNA-AFAP1-AS1.

Cucurbitacin B (CuB) is a natural tetracyclic triterpene product that displays antitumor activity against a wide variety of cancers. In this study, we explored the antipancreatic cancer activity of CuB via the inhibition of expression of the cancer-related long noncoding RNA, actin filament-associated protein 1-antisense RNA 1 (AFAP1-AS1). CuB arrested pancreatic cancer (PC) cells in the G2/M cell cycle phase by suppressing the expression of AFAP1-AS1. Insights into the mechanisms of competing endogenous RNAs (ceRNAs) gained from bioinformatics analysis and luciferase activity assays showed that the epidermal growth factor receptor (EGFR) and AFAP1-AS1 directly compete for miR-146b-5p binding. CuB-induced high miR-146b-5p expression and inhibited the expression of AFAP1-AS1. In summary, reducing the expression of endogenous AFAP1-AS1 effectively increased the available concentration of miR-146b-5p in PC, whereas miR-146b-5p overexpression prevented the expression of endogenous AFAP1-AS1. In particular, we hypothesized that AFAP1-AS1 might act as a ceRNA, effectively becoming a sponge for miR-146b-5p, thereby activating the expression of the EGFR. Thus, CuB suppresses the proliferation, in vitro and in vivo, of PC cells through the ceRNA effect of AFAP1-AS1 on miR-146b-5p.

Cucurbitacin B and SCH772984 exhibit synergistic anti-pancreatic cancer activities by suppressing EGFR, PI3K/Akt/mTOR, STAT3 and ERK signaling.

Cucurbitacin B (CuB) is a natural tetracyclic triterpene product and displays antitumor activity across a wide array of cancers. In this study, we explored the anti-pancreatic cancer activity of CuB alone and in combination with SCH772984, an ERK inhibitor, in vitro and in vivo. CuB inhibited proliferation of pancreatic cancer cells by arresting them in the G2/M cell cycle phase. This was associated with inhibition of EGFR expression and activity and downstream signaling, including PI3K/Akt/mTOR and STAT3. Interestingly, ERK activity was markedly enhanced by activating AMPK signaling after 12 h of CuB treatment. SCH772984 potentiates the cytotoxic effect of CuB on pancreatic cancer cells through complementary inhibition of EGFR, PI3K/Akt/mTOR, STAT3 and ERK signaling, followed by an increase in the pro-apoptotic protein Bim and a decrease in the anti-apoptotic proteins Mcl-1, Bcl-2, Bcl-xl and survivin. Furthermore, combined therapy with CuB and SCH772984 resulted in highly significant growth inhibition of pancreatic cancer xenografts. These results may provide a basis for further development of combining CuB and ERK inhibitors to treat pancreatic cancer.