Targeted delivery of MerTK protein via cell membrane engineered nanoparticle enhances efferocytosis and attenuates atherosclerosis in diabetic ApoE-/- Mice.

BACKGROUND: Clearance of apoptotic cells by efferocytosis is crucial for prevention of atherosclerosis progress, and impaired efferocytosis contributes to the aggravated atherosclerosis. RESULTS: In this study, we found that diabetic ApoE-/- mice showed aggravated atherosclerosis as hyperglycemia damaged the efferocytosis capacity at least partially due to decreased expression of Mer tyrosine kinase (MerTK) on macrophages. To locally restore MerTK in the macrophages in the plaque, hybrid membrane nanovesicles (HMNVs) were thus developed. Briefly, cell membrane from MerTK overexpressing RAW264.7 cell and transferrin receptor (TfR) overexpressing HEK293T cell were mixed with DOPE polymers to produce nanovesicles designated as HMNVs. HMNVs could fuse with the recipient cell membrane and thus increased MerTK in diabetic macrophages, which in turn restored the efferocytosis capacity. Upon intravenous administration into diabetic ApoE-/- mice, superparamagnetic iron oxide nanoparticles (SMN) decorated HMNVs accumulated at the aorta site significantly under magnetic navigation, where the recipient macrophages cleared the apoptotic cells efficiently and thus decreased the inflammation. CONCLUSIONS:  Our study indicates that MerTK decrease in macrophages contributes to the aggravated atherosclerosis in diabetic ApoE-/- mice and regional restoration of MerTK in macrophages of the plaque via HMNVs could be a promising therapeutic approach.

Integration of transcriptome, gut microbiota, and physiology reveals toxic responses of the red claw crayfish (Cherax quadricarinatus) to imidacloprid.

Imidacloprid enters the water environment through rainfall and causes harm to aquatic crustaceans. However, the potential chronic toxicity mechanism of imidacloprid in crayfish has not been comprehensively studied. In this study, red claw crayfish (Cherax quadricarinatus) were exposed to 11.76, 35.27, or 88.17 µg/L imidacloprid for 30 days, and changes in the physiology and biochemistry, gut microbiota, and transcriptome of C. quadricarinatus and the interaction between imidacloprid, gut microbiota, and genes were studied. Imidacloprid induced oxidative stress and decreased growth performance in crayfish. Imidacloprid exposure caused hepatopancreas damage and decreased serum immune enzyme activity. Hepatopancreatic and plasma acetylcholine decreased significantly in the 88.17 µg/L group. Imidacloprid reduced the diversity of the intestinal flora, increased the abundance of harmful flora, and disrupted the microbiota function. Transcriptomic analysis showed that the number of up-and-down-regulated differentially expressed genes (DEGs) increased significantly with increasing concentrations of imidacloprid. DEG enrichment analyses indicated that imidacloprid inhibits neurotransmitter transduction and immune responses and disrupts energy metabolic processes. Crayfish could alleviate imidacloprid stress by regulating antioxidant and detoxification-related genes. A high correlation was revealed between GST, HSPA1s, and HSP90 and the composition of gut microorganisms in crayfish under imidacloprid stress. This study highlights the negative effects and provides detailed sequencing data from transcriptome and gut microbiota to enhance our understanding of the molecular toxicity of imidacloprid in crustaceans.

MARS: a motif-based autoregressive model for retrosynthesis prediction.

MOTIVATION: Retrosynthesis is a critical task in drug discovery, aimed at finding a viable pathway for synthesizing a given target molecule. Many existing approaches frame this task as a graph-generating problem. Specifically, these methods first identify the reaction center, and break a targeted molecule accordingly to generate the synthons. Reactants are generated by either adding atoms sequentially to synthon graphs or by directly adding appropriate leaving groups. However, both of these strategies have limitations. Adding atoms results in a long prediction sequence that increases the complexity of generation, while adding leaving groups only considers those in the training set, which leads to poor generalization. RESULTS: In this paper, we propose a novel end-to-end graph generation model for retrosynthesis prediction, which sequentially identifies the reaction center, generates the synthons, and adds motifs to the synthons to generate reactants. Given that chemically meaningful motifs fall between the size of atoms and leaving groups, our model achieves lower prediction complexity than adding atoms and demonstrates superior performance than adding leaving groups. We evaluate our proposed model on a benchmark dataset and show that it significantly outperforms previous state-of-the-art models. Furthermore, we conduct ablation studies to investigate the contribution of each component of our proposed model to the overall performance on benchmark datasets. Experiment results demonstrate the effectiveness of our model in predicting retrosynthesis pathways and suggest its potential as a valuable tool in drug discovery. AVAILABILITY AND IMPLEMENTATION: All code and data are available at https://github.com/szu-ljh2020/MARS.

Toward Ultrasound Molecular Imaging of Endothelial Dysfunction in Diabetes: Targets, Strategies, and Challenges.

Diabetes vasculopathy is a significant complication of diabetes mellitus (DM), and early identification and timely intervention can effectively slow the progression. Accumulating studies have shown that diabetes causes vascular complications directly or indirectly through a variety of mechanisms. Direct imaging of the endothelial molecular changes not only identifies the early stage of diabetes vasculopathy but also sheds light on the precise treatment. Targeted ultrasound contrast agent (UCA)-based ultrasound molecular imaging (UMI) can noninvasively detect the expression status of molecular biomarkers overexpressed in the vasculature, thereby being a potential strategy for the diagnosis and treatment response evaluation of DM. Amounts of efforts have been focused on identification of the molecular targets expressed in the vasculature, manufacturing strategies of the targeted UCA, and the clinical translation for the diagnosis and evaluation of therapeutic efficacy in both micro- and macrovasculopathy in DM. This review summarizes the latest research progress on endothelium-targeted UCA and discusses their promising future and challenges in diabetes vasculopathy theranostics.

Oleic acid triggers burial behavior in a termite population through an odorant binding protein.

Social insects maintain hygienic conditions through their social immunity behaviors. Among these behaviors, burial behavior of termites is central for protecting healthy individuals from corpses. Many factors trigger burial behavior, and it is generally believed that chemicals released by corpses, such as oleic acid, are the most important cues for triggering burial behavior in termites. However, the contribution of the olfactory system to this behavior remains unclear. Here we report an odorant binding protein (OBP) that transports oleic acid and triggers burial behavior in Coptotermes formosanus Shiraki. We demonstrated that CforOBP7 is highly expressed in the antennae of workers. Fluorescent competition binding experiments exhibited that CforOBP7 has a strong affinity for oleic acid. Furthermore, the antennal response to oleic acid was significantly reduced, and oleic acid-triggered burial behavior was also inhibited in CforOBP7-silenced termites. We conclude that CforOBP7 governs the burial behavior of C. formosanus triggered by oleic acid.

Preparation and characterization of egg white protein film incorporated with epigallocatechin gallate and its application on pork preservation.

The aim of this study was to develop the composite films with antioxidant and biodegradable activity based on egg white protein (EWP) and epigallocatechin gallate (EGCG). Water susceptibility, light transmittance, microstructure and antioxidant properties of the composite films without and with EGCG were fully characterized. It was noted that the addition of EGCG might decrease the moisture content, water solubility and swelling capacity. SEM micrographs revealed that discontinuous blocks and rough surfaces were caused by increasing concentration of EGCG, whereas compact and homogeneous particles appeared when the concentration of EGCG reached to 80 µmol/L. Moreover, the biodegradability of the composite films was demonstrated by the soil degradation properties that they can be almost completely degraded within ten days. Experimental results on the application in chilled fresh pork showed that the EWP-based films could play an antioxidant role when incorporated with EGCG, indicating their great potential for food packaging.

scMIC: A Deep Multi-Level Information Fusion Framework for Clustering Single-Cell Multi-Omics Data.

Cell type identification is a crucial step towards the study of cellular heterogeneity and biological processes. Advances in single-cell sequencing technology have enabled the development of a variety of clustering methods for cell type identification. However, most of existing methods are designed for clustering single omic data such as single-cell RNA-sequencing (scRNA-seq) data. The accumulation of single-cell multi-omics data provides a great opportunity to integrate different omics data for cell clustering, but also raise new computational challenges for existing methods. How to integrate multi-omics data and leverage their consensus and complementary information to improve the accuracy of cell clustering still remains a challenge. In this study, we propose a new deep multi-level information fusion framework, named scMIC, for clustering single-cell multi-omics data. Our model can integrate the attribute information of cells and the potential structural relationship among cells from local and global levels, and reduce redundant information between different omics from cell and feature levels, leading to more discriminative representations. Moreover, the proposed multiple collaborative supervised clustering strategy is able to guide the learning process of the core encoding part by learning the high-confidence target distribution, which facilitates the interaction between the clustering part and the representation learning part, as well as the information exchange between omics, and finally obtain more robust clustering results. Experiments on seven single-cell multi-omics datasets show the superiority of scMIC over existing state-of-the-art methods.

Characterization and Antibacterial Properties of Egg White Protein Films Loaded with ε-Polylysine: Evaluation of Their Degradability and Application.

There is an ongoing trend to design new kinds of food packaging materials with excellent properties which are environmentally friendly enough. The aim of this study was to prepare and characterize egg white protein (EWP)-based composite films with and without ε-polylysine (Lys), as well as to compare their physical-chemical properties, structural properties, degradation and antibacterial properties. The results showed that with the addition of Lys, the composite films showed a decreasing tendency of the water permeability due to the enhanced interaction between proteins and water molecules. As indicated by the structural properties, stronger cross-linking and intermolecular interactions happened with increasing concentration of Lys. In addition, the composite films presented excellent antibacterial activities against Escherichia coli and Staphylococcus aureus on chilled pork in the presence of Lys. Therefore, our prepared films might be used as a freshness-keeping material with an application in meat preservation. The biodegradation evaluation demonstrated that the composite films were environmental-friendly and have potential applications in the field of food packaging.

A partially shared joint clustering framework for detecting protein complexes from multiple state-specific signed interaction networks.

Detecting protein complexes is critical for studying cellular organizations and functions. The accumulation of protein-protein interaction (PPI) data enables the identification of protein complexes computationally. Although a great number of computational methods have been proposed to identify protein complexes from PPI networks, most of them ignore the signs of PPIs that reflect the ways proteins interact (activation or inhibition). As not all PPIs imply co-complex relationships, taking into account the signs of PPIs can benefit the identification of protein complexes. Moreover, PPI networks are not static, but vary with the change of cell states or environments. However, existing methods are primarily designed for single-network clustering, and rarely consider joint clustering of multiple PPI networks. In this study, we propose a novel partially shared signed network clustering (PS-SNC) model for identifying protein complexes from multiple state-specific signed PPI networks jointly. PS-SNC can not only consider the signs of PPIs, but also identify the common and unique protein complexes in different states. Experimental results on synthetic and real datasets show that our PS-SNC model can achieve better performance than other state-of-the-art protein complex detection methods. Extensive analysis on real datasets demonstrate the effectiveness of PS-SNC in revealing novel insights about the underlying patterns of different cell lines.

Desmoplastic Small Round Cell Tumor of the Head and Neck: A Clinicopathological, Immunohistochemical and Molecular Analysis of Three Cases with Literature Review.

Desmoplastic small round cell tumor (DSRCT) is a rare aggressive malignancy typically originating from the abdominal or pelvic cavity. DSRCT presenting as a primary head and neck tumor has rarely been described in the literature. We present three cases of DSRCT arising in the head and neck to further characterize its clinicopathological features. All three patients were male and aged 36, 30 and 17 years. The involved sites included the orbit (1 case) and submandibular gland (2 cases). The tumors ranged in size from 2.4 to 3.5 cm (mean, 2.1 cm). Histologically, all tumors showed irregular-shaped, variable-sized nests of small round cells deposited in an abundant desmoplastic stroma. Tumor cells contained scant amounts of eosinophilic cytoplasm and small hyperchromatic nuclei with inconspicuous nucleoli. Immunohistochemically, the tumors were positive for keratin (AE1/AE3) (3/3), desmin (3/3), vimentin (2/2), NSE (1/1) and EMA (1/1). Fluorescence in situ hybridization (FISH) analysis demonstrated the presence of EWSR1 and WT1 rearrangements in all three cases. All patients received surgery and adjuvant chemotherapy and/or radiotherapy. There was no evidence of recurrence and metastasis in two patients, and the third suffered lung metastasis. DSRCT arising in the head and neck represents an extremely rare condition. It is easily mistaken as poorly differentiated carcinoma due to similar morphology and expression of epithelial markers. Immunohistochemistry assay in conjunction with molecular detection of EWSR1::WT1 fusion will be helpful for arriving at an accurate diagnosis to avoid misdiagnosis and inappropriate treatment.

The complete chloroplast genome sequence of Dictamnus albus L.

Dictamnus albus L. refers to a perennial herb with both ornamental and medicinal value. In the present study, we obtained the complete chloroplast genome sequence of D. albus through high-throughput sequencing. The length of the chloroplast genome was 157,139 bp, while the large single-copy and small single-copy regions were 84,478 bp and 18,587 bp, respectively. The pair of inverted repeat sequences was 27,037 bp, and the GC content was 38.5%. A total of 132 genes were annotated, including 87 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. The chloroplast genomes of D. albus and eight species of Rutaceae were subjected to maximum-likelihood phylogenetic tree analysis. D. albus was found to be most closely related to Orixa japonica.

Plexiform Cellular Schwannoma in Infancy and Childhood: A Clinicopathological Study of Seven Cases of an Underrecognized Nerve Sheath Tumor with a Tendency Toward Local Recurrence.

Plexiform cellular schwannoma (PCS) is very rare, and it is not completely understood. We present our experience with 7 additional cases of PCS in infancy and childhood to further characterize its distinctive clinicopathological features. There were 5 females and 2 males with a mean age of 28 months (ranging, 2 months to 8 years). The involved sites included the left forearm (n = 2), sacrococcygeal region (n = 2), retroperitoneum (n = 1), thoracic spinal canal and thoracic cavity (n = 1), and neck (n = 1). Tumor sizes ranged from 3 to 13 cm in maximum diameter (mean, 7.1 cm). Histologically, all tumors consisted of abundant spindle cells arranged in a multinodular or plexiform growth pattern, possessing elongated, hyperchromatic nuclei and pale eosinophilic cytoplasm with indistinct cell margins. Mitotic figures were easily identified, with a mean count of 4 per 10 consecutive high power fields (HPF). Immunohistochemically, all tumors were strongly and diffusely positive for S100 protein, SOX10 and H3K27me3. The Ki-67 index ranged from 5% to 30% (mean, 15%). Follow-up (available in 6 cases) revealed that 5 patients experienced local recurrence and were treated by re-excision. There was no evidence of recurrence and metastasis in 3 patients, and the other 2 were alive with the disease. In conclusion, PCS is an uncommon nerve sheath tumor predominantly occurring in infants and children, featuring a plexiform or multinodular growth pattern and exhibiting a tendency toward local recurrence. PCS is easily mistaken as malignant peripheral nerve sheath tumor (MPNST) due to its locally aggressive behaviors and worrisome features, including hypercellularity, hyperchromatism and high proliferative activity. Increased awareness of its potential occurrence and greater familiarity with its characteristic features are helpful for both clinicians and pathologists to avoid misdiagnosis and unnecessary overtreatment.

GLI1-altered mesenchymal tumor: a clinicopathological and molecular analysis of ten additional cases of an emerging entity.

We report 10 additional cases of GLI1-altered mesenchymal tumor to further delineate its clinicopathological and molecular spectrum. There were seven males and three females with a median age of 31 years (range 1.3 ~ 75 years). Five tumors arose in the oral cavity, one each in the stomach, uterine cervix, elbow, groin, and thigh. Histologically, all cases except one were composed of monomorphic round to epithelioid cells showing an infiltrative multinodular growth pattern. The neoplastic cells were surrounded by a rich network of capillary vessels. Vessel invasion or subendothelial protrusion into the vascular space was commonly present. One tumor developed regional lymph node metastasis. The remaining case showed a predominantly spindle cell tumor. By immunohistochemistry, most tumors showed diffuse staining of CD56 (8/8) with variable expression of S100 protein (7/8). In three tumors harboring amplified genes, strong and diffuse nuclear staining of MDM2 (2/3) and CDK4 (3/3) were noted. Next-generation sequencing (NGS) studies revealed GLI1 fusions in 7 cases and GLI1 amplification in 2 cases, which were validated by fluorescence in situ hybridization (FISH) analysis in the majority of cases. One case did not show fusion gene by RNA-seq, but FISH revealed both amplification and break-apart of GLI1 gene. Follow-up information showed local recurrences in two patients. All other patients remained disease-free at the last follow-up. Our study further demonstrates that mesenchymal tumors with GLI1 alterations represent a distinctive clinicopathological entity. Although the tumor has a propensity for the tongue, it can also arise in somatic soft tissues as well as in visceral organs. Based on the characteristic morphological features and genomic profiles, we propose the term "GLI1-altered mesenchymal tumor" to describe this emerging entity.

Juvenile hyaline fibromatosis: A clinicopathological study of five cases.

Juvenile hyaline fibromatosis (JHF) is an extremely rare autosomal recessive disease that typically presents in infancy or early childhood. Largely due to the rarity, JHF is still not widely recognized by clinicians and pathologists in China. It is not uncommonly to misdiagnose the disease as other types of disorders. In this study, we present our experience with five cases of JHF to enhance the recognition of this rare but distinctive entity. There were 4 males and 1 female, with age at presentation ranging from 5 to 44 years. All patients presented with multiple subcutaneous nodular lesions of varying size in various parts of the body since birth or early childhood. Three patients also had joint involvement. Pathologically, the lesions were poorly circumscribed, located mainly in the dermis and subcutis. All five cases were characterized by abundant homogeneous hyaline-like matrix that differs sharply from the adjacent connective tissue, which stained strongly with periodic acid-Schiff (PAS) and was diastase resistant. Embedded within the eosinophilic glassy matrix were cords or small clusters of plump spindled to epithelioid cells, frequently with clear cytoplasm. Familiarity with the characteristic features of JHF is not only important in avoiding misdiagnosis but also essential for clinical management and prognostic evaluation.

The stability and antiapoptotic activity of Bm30K-3 can be improved by lysine acetylation in the silkworm, Bombyx mori.

Acetylation is an important, highly conserved, and reversible post-translational modification of proteins. Previously, we showed by nano-HPLC/MS/MS that many nutrient storage proteins in the silkworm are acetylated. Among these proteins, most of the known 30K proteins were shown to be acetylated, including 23 acetylated 30K proteins containing 49 acetylated sites (Kac), indicating the importance of the acetylation of 30K proteins in silkworm. In this study, Bm30K-3, a 30K protein containing three Kac sites, was further assessed in functional studies of its acetylation. Increasing the level of Bm30K-3 acetylation by adding the deacetylase inhibitor trichostatin A (TSA) increased the levels of this protein and further inhibited cellular apoptosis induced by H2 O2 . In contrast, decreasing the level of acetylation by adding the acetylase inhibitor C646 could reduce the level of Bm30K-3 and increase H2 O2 -induced apoptosis. Subsequently, BmN cells were treated with CHX and MG132, and increasing the acetylation level using TSA was shown to inhibit protein degradation and improve the stability of Bm30K-3. Furthermore, the acetylation of Bm30K-3 could compete with its ability to be ubiquitinated, suggesting that acetylation could inhibit the ubiquitin-mediated proteasome degradation pathway, improving the stability and accumulation of proteins in cells. These results further indicate that acetylation might regulate nutrition storage and utilization in Bombyx mori, which requires further study.

[Effects of ursolic acid on c-Cbl-associated protein expression in 3T3-L1 adipocytes with insulin resistance].

OBJECTIVE: To observe the effects of ursolic acid (UA) on insulin resistance and cell differentiation in 3T3-L1 adipocytes and to explore the mechanisms. METHODS: 3T3-L1 adipocytes were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with glucose (25 mmol/L) and insulin (10(-6) mol/L) to induce insulin resistance. After culture, glucose consumption of the adipocytes was detected by glucose oxidase method and glucose uptake was detected by using tritium-marked glucose. Drug concentration for following test was determined through detecting the effects of different concentrations of UA on the activity of 3T3-L1 adipocytes with insulin resistance by methyl thiazolyl tetrazolium (MTT) staining. 3T3-L1 adipocytes with insulin resistance were cultured with DMEM, rosiglitazone, and low- and high-dose UA, and then, glucose uptake and differentiation of 3T3-L1 adipocytes were detected. Finally, real-time fluorescence quantitative polymerase chain reaction and Western blot methods were used to detect the effects of UA on expressions of adipocyte lipid binding protein (aP2), c-Cbl-associated protein (CAP) and matrix metalloproteinase-1 (MMP-1) in 3T3-L1 cells with insulin resistance. RESULTS: After dealing with high glucose/hyperinsulin for 24 h, insulin resistance was induced successfully in the 3T3-L1 adipocytes. The concentrations of UA were defined to be 4 to 20 µmol/L. Compared with the model group, the glucose uptake was significantly increased in the rosiglitazone group and groups treated with low- and high-dose UA (P<0.01). The differentiation levels of 3T3-L1 adipocytes in the UA groups were lower than those in the control group and the rosiglitazone group. Effects of UA on the expressions of aP2 and MMP-1 were not obvious, but UA could up-regulate expression of CAP both in mRNA and protein levels (P<0.01). CONCLUSION: Low- and high-dose UA can improve the glycometabolism and differentiation of 3T3-L1 adipocytes with insulin resistance by up-regulating the expression of CAP.

[Effects of ursolic acid in ameliorating insulin resistance in liver of KKAy mice via peroxisome proliferator-activated receptors α and γ].

OBJECTIVE: To explore the effects and mechanism of ursolic acid in improving hepatic insulin resistance in KKAy mice with spontaneous type 2 diabetes. METHODS: Thirty-five KKAy mice were divided into five groups according to the randomized block design, namely, control, rosiglitazone, fenofibrate, and high- and low-dose ursolic acid groups with seven mice in each group. C57BL/6J mice were used as the normal control group. At the end of the 4th week, free fatty acid (FFA), tumor necrosis factor-α (TNF-α) and adiponectin contents in serum were detected by enzyme-linked immunosorbent assay; the protein expressions of phosphoenolpyruvate carboxykinase (PEPCK), insulin receptor substrate-2 (IRS-2) and glucose transport factor-2 (GLUT-2) were detected by Western blot method; the mRNA expressions of PEPCK, IRS-2 and GLUT-2 were detected by real-time polymerase chain reaction; the expressions of peroxisome proliferator-activated receptor α (PPARα) and peroxisome proliferator-activated receptor γ (PPARγ) in liver tissue were detected by immunohistochemical method. RESULTS: After four weeks of intervention, the contents of FFA, TNF-α and adiponectin in serum of the high-dose ursolic acid group had changed, showing statistically significant difference compared to those of the control group (P<0.01); high dose of ursolic acid had depressant effect on the expressions of PEPCK protein and PEPCK mRNA (P<0.01); low dose of ursolic acid depressed the expression of PEPCK mRNA and induced phosphorylation of IRS-2 in the liver (P<0.05); both high and low dose of ursolic acid improved the expression of PPARα in the liver (P<0.01). CONCLUSION: The effects of ursolic acid in improving hepatic insulin resistance in KKAy mice with spontaneous type 2 diabetes may be closely related to affecting the contents of FFA, TNF-α and adiponectin, improving the expression of PPARα protein, regulating transcription of PEPCK protein and inducing phosphorylation of IRS-2.