This study describes the structure of DNA polymerase I from Thermus phage G20c, termed PolI_G20c. This is the first structure of a DNA polymerase originating from a group of related thermophilic bacteriophages infecting Thermus thermophilus, including phages G20c, TSP4, P74-26, P23-45 and phiFA and the novel phage Tth15-6. Sequence and structural analysis of PolI_G20c revealed a 3'-5' exonuclease domain and a DNA polymerase domain, and activity screening confirmed that both domains were functional. No functional 5'-3' exonuclease domain was present. Structural analysis also revealed a novel specific structure motif, here termed SβαR, that was not previously identified in any polymerase belonging to the DNA polymerases I (or the DNA polymerase A family). The SβαR motif did not show any homology to the sequences or structures of known DNA polymerases. The exception was the sequence conservation of the residues in this motif in putative DNA polymerases encoded in the genomes of a group of thermophilic phages related to Thermus phage G20c. The structure of PolI_G20c was determined with the aid of another structure that was determined in parallel and was used as a model for molecular replacement. This other structure was of a 3'-5' exonuclease termed ExnV1. The cloned and expressed gene encoding ExnV1 was isolated from a thermophilic virus metagenome that was collected from several hot springs in Iceland. The structure of ExnV1, which contains the novel SβαR motif, was first determined to 2.19 Å resolution. With these data at hand, the structure of PolI_G20c was determined to 2.97 Å resolution. The structures of PolI_G20c and ExnV1 are most similar to those of the Klenow fragment of DNA polymerase I (PDB entry 2kzz) from Escherichia coli, DNA polymerase I from Geobacillus stearothermophilus (PDB entry 1knc) and Taq polymerase (PDB entry 1bgx) from Thermus aquaticus.

MicroRNAs (miRNAs) have been revealed to be critical genetic regulators in various physiological processes and thus quantitative information on the expression level of critical miRNAs has important implications for the initiation and development of human diseases, including cancers.

Decalcified bone matrix has great potential and application prospects in the repair of bone defects due to its good biocompatibility and osteogenic activity. In order to verify whether fish decalcified bone matrix (FDBM) has similar structure and efficacy, this study used the principle of HCl decalcification to prepare the FDBM by using fresh halibut bone as the raw material, and then degreasing, decalcifying, dehydrating and freeze-drying it. Its physicochemical properties were analyzed by scanning electron microscopy and other methods, and then its biocompatibility was tested by in vitro and in vivo experiments. At the same time, an animal model of femoral defect in rats was established, and commercially available bovine decalcified bone matrix (BDBM) was used as the control group, and the area of femoral defect in rats was filled with the two materials respectively. The changes in the implant material and the repair of the defect area were observed by various aspects such as imaging and histology, and its osteoinductive repair capacity and degradation properties were studied. The experiments showed that the FDBM is a form of biomaterial with high bone repair capacity and lower economic cost than other related materials such as bovine decalcified bone matrix. FDBM is simpler to extract and the raw materials are more abundant, which can greatly improve the utilization of marine resources. Our results show that FDBM not only has a good repair effect on bone defects, but also has good physicochemical properties, biosafety and cell adhesion, and is a promising medical biomaterial for the treatment of bone defects, which can basically meet the clinical requirements for bone tissue repair engineering materials.

Membrane-based alkaline water electrolyser is promising for cost-effective green hydrogen production. One of its key technological obstacles is the development of active catalyst-materials for alkaline hydrogen-evolution-reaction (HER). Here, we show that the activity of platinum towards alkaline HER can be significantly enhanced by anchoring platinum-clusters onto two-dimensional fullerene nanosheets. The unusually large lattice distance (~0.8 nm) of the fullerene nanosheets and the ultra-small size of the platinum-clusters (~2 nm) leads to strong confinement of platinum clusters accompanied by pronounced charge redistributions at the intimate platinum/fullerene interface. As a result, the platinum-fullerene composite exhibits 12 times higher intrinsic activity for alkaline HER than the state-of-the-art platinum/carbon black catalyst. Detailed kinetic and computational investigations revealed the origin of the enhanced activity to be the diverse binding properties of the platinum-sites at the interface of platinum/fullerene, which generates highly active sites for all elementary steps in alkaline HER, particularly the sluggish Volmer step. Furthermore, encouraging energy efficiency of 74% and stability were achieved for alkaline water electrolyser assembled using platinum-fullerene composite under industrially relevant testing conditions.

The contamination of fermented feeds and foods with fungi and mycotoxins is a major food safety issue worldwide. Certain lactic acid bacteria (LAB), generally recognized as safe (GRAS) fermentation probiotics, are able to reduce microbial and mycotoxins contamination. In this study, Lactiplantibacillus (L.) plantarum Q1-2 and L. salivarius Q27-2 with antifungal properties were screened as inoculants for mixed fermenting feed, and the fermentation and nutritional qualities, microbial community, and mycotoxins of mixed fermented feed were analyzed at different fermentation periods (1, 3, 7, 15, and 30 days, respectively). The findings indicated that the utilization of Q1-2 and Q27-2 strains in fermenting feed led to a decrease in pH and an increase in lactic acid concentration and the proportion of Lactiplantibacillus, while effectively restraining the proliferation of undesirable microorganisms. In particular, Q1-2 reduced the relative abundance of fungi including Fusarium and Aspergillus. Compared to the control group, the Q1-2 and Q27-2 groups reduced aflatoxin B1 by 34.17% and 16.57%, and deoxynivalenol by up to 90.61% and 51.03%. In short, these two LAB inoculants could reduce the contents of aflatoxin B1 and deoxynivalenol to the limited content levels stipulated by the Chinese National Standard GB 13078-2017. These findings suggest that the LAB strains of Q1-2 and Q27-2 have potential applications in the feed industry for the mitigation of mycotoxin pollution, thereby enhancing the quality of animal feed.

Pain is the most common cancer-related symptom, but it is often undertreated. Telemedicine is widely used in cancer treatment, but its effectiveness is uncertain.

Houshiheisan (HSHS), a classic prescription in traditional Chinese medicine (TCM), has shown outstanding efficacy in treating stroke. This study investigated various therapeutic targets of HSHS for ischemic stroke using mRNA transcriptomics. Herein, rats were randomly separated into the sham, model, HSHS 5.25 g/kg (HSHS5.25), and HSHS 10.5 g/kg (HSHS10.5) groups. Rats suffering from stroke were induced by permanent middle cerebral artery occlusion (pMCAO). After seven days of HSHS treatment, behavioral tests were conducted, and histological damage was examined with hematoxylin-eosin (HE). The mRNA expression profiles were identified using microarray analysis and quantitative real-time PCR (qRT-PCR) validated gene expression changes. An analysis of gene ontology and pathway enrichment was conducted to analyze potential mechanisms confirmed using immunofluorescence and western blotting. HSHS5.25 and HSHS10.5 improved neurological deficits and pathological injury in pMCAO rats. The intersections of 666 differentially expressed genes (DEGs) were chosen using transcriptomics analysis in the sham, model, and HSHS10.5 groups. The enrichment analysis suggested that the therapeutic targets of HSHS might regulate the apoptotic process and ERK1/2 signaling pathway, which was related to neuronal survival. Moreover, TUNEL and immunofluorescence analysis indicated that HSHS inhibited apoptosis and enhanced neuronal survival in the ischemic lesion. Western blot and immunofluorescence assay indicated that HSHS10.5 decreased Bax/Bcl-2 ratio and suppressed caspase-3 activation, while the phosphorylation of ERK1/2 and CREB was upregulated in a stroke rat model after HSHS treatment. Effective inhibition of neuronal apoptosis by activating the ERK1/2-CREB signaling pathway may be a potential mechanism for HSHS in the treatment of ischemic stroke.

Osteoarthritis (OA) is the most prevalent joint disease characterized by the degeneration of articular cartilage and the remodeling of its underlying bones, resulting in pain and loss of function in the knees and hips. As far as we know, no curative treatments are available except for the joint replacement. The precise molecular mechanisms which are involved in the degradation of cartilage matrix and development of osteoarthritis are still unclear.

The low-temperature roasting of sesame oil has become increasingly popular because of its nutritional benefits; however, the flavor is reduced. In order to improve the quality of sesame oil without exogenous addition, sesame meal was hydrolyzed and further used to prepare Maillard reaction products (MRPs) while protease hydrolysis (PH) and glucoamylase-protease hydrolysis (GPH) were used, and their respective Maillard products (PHM and GPHM) were added in the oils for reducing sugar and total sugar content determination, free amino acid determination, and color and descriptive sensory analysis, as well as electronic nose, SPME-GC-MS, odor activity value, and oxidative stability analyses. Results showed that the MRPs could be produced using the enzymatically hydrolyzed sesame meal without exogenous addition, and the oil flavor blended with GPHM (GPHM-SO) was significantly (p < 0.05) improved with the best sensory quality. The composition of pyrazines (119.35 μg/mL), furans (13.95 μg/mL), and sulfur substances (6.25 μg/mL) contributed positively to sensory properties in GPHM-SO, and 2,5-dimethylpyrazine, 2,6-dimethylpyrazine, and 2,3-dimethylpyrazine were characterized as the key flavor compounds with odor activity values of 7.01, 14.80, and 31.38, respectively. Furthermore, the oxidative stability of the oil was significantly improved with the addition of MRPs, and the shelf life of GPHM-SO was predicted to be extended by 1.9 times more than that of the crude oil based on the accelerated oxidation fitting analysis. In general, the MRPs derived only from sesame meal can enhance the flavor and oxidative stability of sesame oil and can be applied in the oil industry.

The recognition of pharmacological substances, compounds and proteins is essential for biomedical relation extraction, knowledge graph construction, drug discovery, as well as medical question answering. Although considerable efforts have been made to recognize biomedical entities in English texts, to date, only few limited attempts were made to recognize them from biomedical texts in other languages. PharmaCoNER is a named entity recognition challenge to recognize pharmacological entities from Spanish texts. Because there are currently abundant resources in the field of natural language processing, how to leverage these resources to the PharmaCoNER challenge is a meaningful study.

The study was to explore the effect of subintimal angioplasty (SIA) on the levels of soluble intercellular adhesion molecule-1 (sICAM-1) and vascular endothelial cadherin (VE-cadherin) in the rabbit model of lower extremity arterial occlusion. Specifically, the poly(N-isopropylacrylamide-co-butyl methacrylate) (PIB) temperature-sensitive nanogel was prepared, and the cytotoxicity of direct and indirect contact with PIB temperature-sensitive gel was analyzed then. Subsequently, the PIB temperature-sensitive gel was injected to the New Zealand white rabbit to prepare the lower extremity arterial occlusion model. The healthy control, model group, and SIA group were compared for the serum lipids, fibrinogen (Fbg), fibrinogen (Fbg), and fibrinogen (Fbg) levels. The results showed that the cell proliferation activity and survival rate were always higher than 90% under different concentrations of PIB temperature-sensitive gels. Compared with the model group, the SIA group had increased total cholesterol (TC), triglycerides (TG), low-density lipoprotein (LDL), and Fbg levels, but decreased high-density lipoprotein (HDL) level (P < 0.05); decreased TXB2, ET-1, and ICAM-1 levels, but increased levels of 6-Keto-PGF1α and NO (P < 0.05); and decreased sICAM-1 and VE-cadherin levels (P < 0.05). It showed that PIB temperature-sensitive nanogel can elicit vascular embolism, and SIA is suggested in the treatment of lower extremity arterial occlusion.

Irradiation-induced immunosuppression often occurs during radiotherapy in patients, which would increase the risk of opportunistic infections. Many Chinese herbal prescriptions or natural extracts have recently attracted increased radiation protection and therapy attention due to their low toxicity.

Aohan fine-wool sheep (AFWS) is a high-quality fine-wool sheep breed that supplies wool and meat. Research is needed on the molecular mechanism behind intramuscular fat (IMF) deposition that greatly improves mutton quality. The widely expressed non-coding RNA is physiologically used in roles such as competitive endogenous RNA (ceRNA) that includes circular RNAs (circRNAs). Although circRNAs were studied in many fields, little research was devoted to IMF in sheep. We used the longissimus dorsi muscle of 2 and 12-month-old AWFS as research material to identify circRNAs related to IMF deposition in these sheep by RNA-seq screening for differentially expressed circRNAs in the two age groups. A total of 11,565 candidate circRNAs were identified, of which the 104 differentially expressed circRNAs in the two age groups were analyzed. Enrichment analysis was performed using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes. The enriched pathways included lipid transport (GO:0006869), negative regulation of canonical Wnt signaling pathway (GO:0090090), fat digestion and absorption (ko04975), and sphingolipid metabolism (ko00600). The differentially expressed circRNAs included ciRNA455, circRNA9086, circRNA7445, circRNA4557, and others. The source genes involved in these pathways might regulate IMF deposition. We used the TargetScan and miRanda software for interaction analysis, and a network diagram of circRNA-miRNA interactions was created. CircRNA455-miR-127, circRNA455-miR-29a, circRNA455-miR-103, circRNA4557-mir149-5p, and circRNA2440-mir-23a might be involved in the IMF deposition process. The targeting relationship of circRNA4557-miR-149-5p was verified by a dual-luciferase reporter assay. The RT-qPCR results of seven randomly selected circRNAs were consistent with the sequencing results. This study provides additional information on circRNA regulation of IMF deposition in AFWS and is a useful resource for future research on this sheep breed.

Trillium tschonoskii Maxim. (TTM), is a perennial herb from Liliaceae, that has been widely used as a traditional Chinese medicine treating cephalgia and traumatic hemorrhage. The present work was designed to investigate whether the total saponins from Trillium tschonoskii Maxim. (TSTT) would promote brain remodeling and improve gait impairment in the chronic phase of ischemic stroke. A focal ischemic model of male Sprague-Dawley (SD) rats was established by permanent middle cerebral artery occlusion (MCAO). Six hours later, rats were intragastrically treated with TSTT (120, 60, and 30 mg/kg) and once daily up to day 30. The gait changes were assessed by the CatWalk-automated gait analysis system. The brain tissues injuries, cerebral perfusion and changes of axonal microstructures were detected by multimodal magnetic resonance imaging (MRI), followed by histological examinations. The axonal regeneration related signaling pathways including phosphatidylinositol 3-kinases (PI3K)/protein kinase B (AKT)/glycogen synthase kinase-3 (GSK-3)/collapsin response mediator protein-2 (CRMP-2) were measured by western blotting. TSTT treatment significantly improved gait impairment of rats. MRI analysis revealed that TSTT alleviated tissues injuries, significantly improved cerebral blood flow (CBF), enhanced microstructural integrity of axon and myelin sheath in the ipsilesional sensorimotor cortex and internal capsule. In parallel to MRI findings, TSTT preserved myelinated axons and promoted oligodendrogenesis. Specifically, TSTT interventions markedly up-regulated expression of phosphorylated GSK-3, accompanied by increased expression of phosphorylated PI3K, AKT, but reduced phosphorylated CRMP-2 expression. Taken together, our results suggested that TSTT facilitated brain remodeling. This correlated with improving CBF, encouraging reorganization of axonal microstructure, promoting oligodendrogenesis and activating PI3K/AKT/GSK-3/CRMP-2 signaling, thereby improving poststroke gait impairments.

In most grapevine planting regions, especially in south of China, plenty of rainfall and high water level underground are the characteristic of the area, a series of problem during fruit ripening easily caused poor color quality. Thereby affecting fruit quality, yield and economic benefits. The accumulation of anthocyanin is regulated by transcriptional regulatory factor and a series of cultivation measures, root restriction can make plants in the environment of stress and stress relief, root restriction induced the higher expression of VvMYB15 and VvWRKY40, and consistent with anthocyanin accumulation. Whether and how root restriction-inducible VvMYB15 and VvWRKY40 transcription factor regulate anthocyanin synthesis in grape berry is still unclear. In this study, we identified that the transient overexpression of VvMYB15 and VvWRKY40 alone or both in strawberry fruits and grape berries can promote anthocyanin accumulation and increase the expression level of anthocyanin biosynthetic genes, indicating VvMYB15 and VvWRKY40 play a positive regulator of anthocyanin biosynthesis. Furthermore, we confirmed that both VvMYB15 and VvWRKY40 specifically bind to the promoter region of VvF3'5'H and VvUFGT, and the expression of VvF3'5'H and VvUFGT is further activated through the heterodimer formation between VvMYB15 and VvWRKY40. Finally, we confirmed that VvMYB15 promoted anthocyanin accumulation by interacting with VvWRKY40 in grape berries, our findings provide insights into a mechanism involving the synergistic regulation of root restriction-dependent coloration and biosynthesis via a VvMYB15 and VvWRKY40 alone or both in grape berries.

Background: Irreversible worsening of cardiac function is an adverse event associated with significant morbidity among patients with acute decompensated heart failure (ADHF). We aimed to develop a parsimonious model which is simple to use in clinical settings for the prediction of the risk of irreversible worsening of cardiac function. Methods: A total of 871 ADHF patients were enrolled in this study. Data for each patient were collected from the medical records. Irreversible worsening of cardiac function included cardiac death within 30-days of patient hospitalization, implantation of a left ventricular assistance device, or emergency heart transplantation. We performed LASSO regression for variable selection to derive a multivariable logistic regression model. Five candidate predictors were selected to derive the final prediction model. The prediction model was verified using C-statistics, calibration curve, and decision curve. Results: Irreversible worsening of cardiac function occurred in 7.8% of the patients. Advanced age, NYHA class, high blood urea nitrogen, hypoalbuminemia, and vasopressor use were its strongest predictors. The prediction model showed good discrimination C-statistic value, 0.866 (95% CI, 0.817-0.907), which indicated good identical calibration and clinical efficacy. Conclusion: In this study, we developed a prediction model and nomogram to estimate the risk of irreversible worsening of cardiac function among ADHF patients. The findings may provide a reference for clinical physicians for detection of irreversible worsening of cardiac function and enable its prompt management.

Increased intracellular iron spurs mitochondrial biogenesis and respiration to satisfy high-energy demand during osteoclast differentiation and bone-resorbing activities. Transferrin receptor 1 (Tfr1) mediates cellular iron uptake through endocytosis of iron-loaded transferrin, and its expression increases during osteoclast differentiation. Nonetheless, the precise functions of Tfr1 and Tfr1-mediated iron uptake in osteoclast biology and skeletal homeostasis remain incompletely understood. To investigate the role of Tfr1 in osteoclast lineage cells in vivo and in vitro, we crossed Tfrc (encoding Tfr1)-floxed mice with Lyz2 (LysM)-Cre and Cathepsin K (Ctsk)-Cre mice to generate Tfrc conditional knockout mice in myeloid osteoclast precursors (Tfr1ΔLysM) or differentiated osteoclasts (Tfr1ΔCtsk), respectively. Skeletal phenotyping by µCT and histology unveiled a significant increase in trabecular bone mass with normal osteoclast number in long bones of 10-week-old young and 6-month-old adult female but not male Tfr1ΔLysM mice. Although high trabecular bone volume in long bones was observed in both male and female Tfr1ΔCtsk mice, this phenotype was more pronounced in female knockout mice. Consistent with this gender-dependent phenomena, estrogen deficiency induced by ovariectomy decreased trabecular bone mass in Tfr1ΔLysM mice. Mechanistically, disruption of Tfr1 expression attenuated mitochondrial metabolism and cytoskeletal organization in mature osteoclasts in vitro by attenuating mitochondrial respiration and activation of the Src-Rac1-WAVE regulatory complex axis, respectively, leading to decreased bone resorption with little impact on osteoclast differentiation. These results indicate that Tfr1-mediated iron uptake is specifically required for osteoclast function and is indispensable for bone remodeling in a gender-dependent manner.

Pancreatic adenocarcinoma (PAAD) has become one of the deadliest malignancies in the world. Since necroptosis plays a crucial role in regulating the immune system, it is necessary to develop novel prognostic biomarkers associated with necroptosis and explore its potential role in PAAD. The transcriptome RNA-seq data of PAAD were downloaded from the TCGA and GTEx databases. A prognostic signature was constructed by the least absolute shrinkage and selection operator (LASSO) Cox regression, and its prognostic value was evaluated by nomogram and validated in an independent GEO cohort. We identified a total of 24 differentially expressed NRGs in PAAD, and constructed a prognostic signature with 5 NRGs, which showed good performance in predicting the prognosis of PAAD patients. The ROC curves for 1-, 3-, and 5-year survival rate were 0.652, 0.778, and 0.817, respectively. This prognostic signature showed consistent prognosis prediction in an independent patient cohort. Furthermore, the correlations between 5-NRGs signature and TMB, MSI, histopathological classification, immune infiltration, immune types, and immunomodulators were all significant. Notably, the expression profiles of the five NRGs in exosomes of serum were consistent with their expression in tumor tissues. These data suggested that the 5-NRGs signature is a promising biomarker for predicting the prognosis of PAAD.

Circular RNAs (circRNAs) belong to a novel class of noncoding RNA that gained more attention in human cancer pathogenesis. The role of circRNA in esophageal squamous cell carcinoma (ESCC) is largely unclear. Present investigation was to characterize new circRNAs regulating ESCC progression and explore the regulatory mechanisms in ESCC. In this study, circRNAs differentially expressed in ESCC and adjacent normal tissues were characterized via high-throughput sequencing. Then the differentially expressed circRNA between ESCC and adjacent normal tissues were investigated using Rt-qPCR. The role of circ-ARAP2 expression on tumor progression were detected in both in vivo and in vitro. Luciferase reporter assays were used to identify the relationships among circ-ARAP2, microRNA (miR)-761 and the cell cycle regulator Forkhead Box M1 (FOXM1). The result of the expression profile analyses regarding human circRNAs in ESCC demonstrated that circ-ARAP2 was up-regulated significantly in both ESCC tissues and cell lines. Downregulation circ-ARAP2 suppressed ESCC proliferation, tumor growth and metastasis in both in vivo and in vitro. The data also suggested that miR-761 and FOXM1 were circ-ARAP2 downstream targets which were confirmed through luciferase reporter analysis. Overexpression of FOXM1 or inhibiting miR-761 restored ESCC cell proliferation and invasion ability after silencing circ-ARAP2. The study also found that circ-ARAP2 influenced the endothelial-mesenchymal transition (EMT) and cancer stem cells differently by regulating miR-761/FOXM1. In one word, the results demonstrated that abnormal circ-ARAP2 expression promoted ESCC progression by regulating miR-761/FOXM1 axis-mediated stemness and EMT.

Bladder urothelial carcinoma (BLCA) is a complex disease with high morbidity and mortality. Changes in alternative splicing (AS) and splicing factor (SF) can affect gene expression, thus playing an essential role in tumorigenesis. This study downloaded 412 patients' clinical information and 433 samples of transcriptome profiling data from TCGA. And we collected 48 AS signatures from SpliceSeq. LASSO and Cox analyses were used for identifying survival-related AS events in BLCA. Finally, 1,645 OS-related AS events in 1,129 genes were validated by Kaplan-Meier (KM) survival analysis, ROC analysis, risk curve analysis, and independent prognostic analysis. Finally, our survey provides an AS-SF regulation network consisting of five SFs and 46 AS events. In the end, we profiled genes that AS occurred in pan-cancer and five SFs' expression in tumor and normal samples in BLCA. We selected CLIP-seq data for validation the interaction regulated by RBP. Our study paves the way for potential therapeutic targets of BLCA.