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The colchicine site of β-tubulin has been proven to be essential binding sites of microtubule polymerization inhibitors. Recent studies implied that GTP pocket of α-tubulin adjacent to colchicine sites is a potential binding site for developing tubulin polymerization inhibitors. However, the structural basis for which type of structural fragments was more beneficial for enhancing the affinity of α-tubulin is still unclear. Here, podophyllotoxin derivatives-tubulin complex crystals indicated that heterocyclic with the highly electronegative and small steric hindrance was conducive to change configuration and enhance the affinity of the residues in GTP pocket of α-tubulin. Triazole with lone-pairs electrons and small steric hindrance exhibited the strongest affinity for enhancing affinity of podophyllotoxin derivatives by forming two hydrogen bonds with αT5 Ser178. Pyrimidine with the secondary strong affinity could bind Asn101 to make the αH7 configuration deflection, which reduces the stability of tubulin result in its depolymerization. Conversely, 4β-quinoline-podophyllotoxin with the weakest affinity did not interact with α-tubulin. The molecular dynamics simulation and protein thermal shift results showed that 4β-triazole-podophyllotoxin-tubulin was the most stable mainly due to two hydrogen bonds and the higher van der Waals force. This work provided a structural basis of the potential binding sites for extending the α/β-tubulin dual-binding sites inhibitors design strategy., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Ya-Jie Tang reports financial support was provided by the National Key R&D Program of China (No. 2019YFA0905700). Wei Zhao and Hong-Mei Li reports financial support was provided by the National Key R&D Program of China (2021YFC2101500). Ya-Jie Tang reports financial support was provided by the National Natural Science Foundation for Distinguished Young Scholars (No. 21625602), the National Natural Science Foundation of China (No. 21838002). Ya-Jie Tang reports financial support was provided by the Program of Shandong for Taishan Scholars (No. tspd20221101). Ya-Jie Tang reports financial support was provided by the Foundation for Innovative Research Groups of State Key Laboratory of Microbial Technology (WZCX2021–03). If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The intestinal tract plays a vital role in both digestion and immunity, making its equilibrium crucial for overall health. This equilibrium relies on the dynamic interplay among intestinal epithelial cells, macrophages, and crypt stem cells. Intestinal epithelial cells play a pivotal role in protecting and regulating the gut. They form vital barriers, modulate immune responses, and engage in pathogen defense and cytokine secretion. Moreover, they supervise the regulation of intestinal stem cells. Macrophages, serving as immune cells, actively influence the immune response through the phagocytosis of pathogens and the release of cytokines. They also contribute to regulating intestinal stem cells. Stem cells, known for their self-renewal and differentiation abilities, play a vital role in repairing damaged intestinal epithelium and maintaining homeostasis. Although research has primarily concentrated on the connections between epithelial and stem cells, interactions with macrophages have been less explored. This review aims to fill this gap by exploring the roles of the intestinal epithelial-macrophage-crypt stem cell axis in maintaining intestinal balance. It seeks to unravel the intricate dynamics and regulatory mechanisms among these essential players. A comprehensive understanding of these cell types' functions and interactions promises insights into intestinal homeostasis regulation. Moreover, it holds potential for innovative approaches to manage conditions like radiation-induced intestinal injury, inflammatory bowel disease, and related diseases., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Renal fibrosis is a common outcome of various renal injuries, leading to structural destruction and functional decline of the kidney, and is also a critical prognostic indicator and determinant in renal diseases therapy. Hypoxia is induced in different stress and injuries in kidney, and the hypoxia inducible factors (HIFs) are activated in the context of hypoxia in response and regulation the hypoxia in time. Under stress and hypoxia conditions, HIF-1α increases rapidly and regulates intracellular energy metabolism, cell proliferation, apoptosis, and inflammation. Through reprogramming cellular metabolism, HIF-1α can directly or indirectly induce abnormal accumulation of metabolites, changes in cellular epigenetic modifications, and activation of fibrotic signals. HIF-1α protein expression and activity are regulated by various posttranslational modifications. The drugs targeting HIF-1α can regulate the downstream cascade signals by inhibiting HIF-1α activity or promoting its degradation. As the renal fibrosis is affected by renal diseases, different diseases may trigger different mechanisms which will affect the therapy effect. Therefore, comprehensive analysis of the role and contribution of HIF-1α in occurrence and progression of renal fibrosis, and determination the appropriate intervention time of HIF-1α in the process of renal fibrosis are important ideas to explore effective treatment strategies. This study reviews the regulation of HIF-1α and its mediated complex cascade reactions in renal fibrosis, and lists some drugs targeting HIF-1α that used in preclinical studies, to provide new insight for the study of the renal fibrosis mechanism., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Background: Cancer-associated fibroblasts (CAFs) play pivotal roles in tumor invasion and metastasis. However, studies on CAF biomarkers in Cutaneous Melanoma (CM) are still scarce. This study aimed to explore the potential CAF biomarkers in CM, propose the potential therapeutic targets, and provide new insights for targeted therapy of CAFs in CM., Methods: We utilized weighted gene co-expression network analysis to identify CAF signature genes in CM, and conducted comprehensive bioinformatics analysis on the CAF risk score established by these genes. Moreover, single-cell sequencing analysis, spatial transcriptome analysis, and cell experiments were utilized for verifying the expression and distribution pattern of signature genes. Furthermore, molecular docking was employed to screen potential target drugs., Results: FBLN1 and COL5A1, two crucial CAF signature genes, were screened to establish the CAF risk score. Subsequently, a comprehensive bioinformatic analysis of the CAF risk score revealed that high-risk score group was significantly enriched in pathways associated with tumor progression. Besides, CAF risk score was significantly negatively correlated with clinical prognosis, immunotherapy response, and tumor mutational burden in CM patients. In addition, FBLN1 and COL5A1 were further identified as CAF-specific biomarkers in CM by multi-omics analysis and experimental validation. Eventually, based on these two targets, Mifepristone and Dexamethasone were screened as potential anti-CAFs drugs., Conclusion: The findings indicated that FBLN1 and COL5A1 were the CAF signature genes in CM, which were associated with the progression, treatment, and prognosis of CM. The comprehensive exploration of CAF signature genes is expected to provide new insight for clinical CM therapy., Competing Interests: Declaration of competing interest All the authors declare that they have no conflict of interest regarding the publication of the paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

DNA damage caused by internal or external factors lead to increased genomic instability and various diseases. The DNA damage response (DDR) is a crucial mechanism that maintaining genomic stability through detecting and repairing DNA damage timely. Post-translational modifications (PTMs) play significant roles in regulation of DDR. Among the present PTMs, crotonylation has emerged as a novel identified modification that is involved in a wide range of biological processes including gene expression, spermatogenesis, cell cycle, and the development of diverse diseases. In the past decade, numerous crotonylation sites have been identified in histone and non-histone proteins, leading to a more comprehensive and deep understanding of the function and mechanisms in protein crotonylation. This review provides a comprehensive overview of the regulatory mechanisms of protein crotonylation and the effect of crotonylation in DDR. Furthermore, the effect of protein crotonylation in tumor development and progression is presented, to inspire and explore the novel strategies for tumor therapy., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Gastric cancers, with gastric adenocarcinoma (GAC) as the most common histological type, cause quite a few of deaths. In order to improve the survival rate after GAC treatment, it is important to develop a method for early detection and therapy support of GAC. Raman spectroscopy is a potential tool for probing cancer cell due to its real-time and non-destructive measurements without any additional reagents. In this study, we use Raman spectroscopy to examine GAC samples, and distinguish cancerous gastric mucosa from normal gastric mucosa. Average Raman spectra of two groups show differences at 750 cm -1 , 1004 cm -1 , 1449 cm -1 , 1089-1128 cm -1 , 1311-1367 cm -1 and 1585-1665 cm -1 , These peaks were assigned to cytochrome c, phenylalanine, phospholipid, collagen, lipid, and unsaturated fatty acid respectively. Furthermore, we build a SENet-LSTM model to realize the automatic classification of cancerous gastric mucosa and normal gastric mucosa, with all preprocessed Raman spectra in the range of 400-1800 cm -1 as input. An accuracy 96.20% was achieved. Besides, by using masking method, we found the Raman spectral features which determine the classification and explore the explainability of the classification model. The results are consistent with the conclusions obtained from the average spectrum. All results indicate it is potential for pre-cancerous screening to combine Raman spectroscopy and machine learning., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Introduction: Previous studies have shown that diffuse large B-cell lymphoma (DLBCL) subtype with both B-cell antigen receptor complex-associated protein beta chain (CD79B) and myeloid differentiation primary response 88 mutations (MYD88) had inferior outcome under standard immunochemotherapy. However, the prognostic significance of CD79B alone in DLBCL has not been fully elucidated. We conducted a meta-analysis to investigate the role of CD79B mutation on overall survival (OS) in patients with DLBCL., Methods: We performed literature search in PubMed and Embase databases and followed PRISMA guidelines to select publications for analysis. The primary and secondary outcome was OS and progression-free survival (PFS) respectively. Hazard ratio (HR) for OS/PFS in CD79B mutant group with that in wild-type group in R-chemotherapy patients was either estimated using Cox proportional hazard model from the studies with individual participant level data or extracted from the original publication with aggregated results., Results: Nine eligible studies with survival information according to CD79B mutation status were included in this meta-analysis. The pooled hazard ratio for OS was 1.38 (95% CI, 1.13-1.70; p = 0.0021) for CD79B mutation, providing evidence that CD79B mutation was unfavorable prognostic factor for survival in DLBCL patients treated with immunochemotherapy. We identified the inferior prognostic impact of CD79B mutation was independent from well-established prognostic model in DLBCL, International Prognostic Index. The predictive power of CD79B mutation was stronger than that of MYD88 mutation., Conclusion: This meta-analysis revealed that CD79B mutation could be a key biomarker for DLBCL disease progression and future mechanism-based target therapy in DLBCL needs to be studied., (Copyright © 2022. Published by Elsevier Inc.)

Antimicrobial triclosan (TCS), one of the popular ingredients added to sanitizing products, has widespread use in personal care. However, it poses potential risks to reproduction and development. Unfortunately, the underlying mechanisms remain largely unclear. This study aimed to investigate effects of TCS on the development of preimplantation mouse embryo and explore related mechanisms Mouse zygotes were collected and cultured to blastocysts in KSOM medium supplemented with four different concentrations of TCS. The development rates, pluripotency or stem cells markers, and microRNA (miR)- 134 were compared between control and experimental groups across each specific developmental stage. Prolonged exposure to TCS remarkably impaired early embryo development in vitro by hampering morula and blastocyst formations (P < 0.05, P < 0.001). The arrest of embryo development was linked with decreased expressions of pluripotency or stem cells markers, especially Nanog and Notch1. Moreover, based on miRWalk database and in vitro luciferase assays, we confirmed that miR-134 induced by TCS was a negative regulator of Nanog. Crucially, impaired TCS-treated embryos could be rescued by inhibiting miR-134 or forced overexpressing Nanog mRNA. Altogether, our results highlight that pathologically relevant level of TCS compromises preimplantation mouse embryo development by inducing miR-134 and triggering miR-134/Nanog axis. Considering high conservative of miR-134 between human and mouse, it should be the most promising potential target to regulate development of preimplantation embryo., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Xiufeng Ling reports financial support was provided by The National Natural Science Foundation. Chun Zhao reports financial support was provided by The National Natural Science Foundation. Ye yang reports financial support was provided by The National Natural Science Foundation., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Emerging data have suggested the potential role of prenatal PM 2.5 exposure as a neurotoxin for offspring. However, the existing results are equivocal, and no study has examined the effects of complex chemical constituents of the particular matter on offspring neurodevelopment. Therefore, in a prospective birth cohort study conducted in Jiangsu, China, we aimed to investigate the association between prenatal exposure to PM 2.5 and the neurodevelopment in infants, and further assess the effects of specific chemical constituents of PM 2.5 . A total of 1531 children who had available data on daily prenatal PM 2.5 exposure and completed assessment on neurodevelopment at 1 year old were enrolled. We used the high-performance machine-learning model to estimate daily PM 2.5 exposure concentrations at 1 km × 1 km spatial resolution. The combined geospatial-statistical model was applied to evaluate average concentrations of six chemical constituents [organic matter (OM), black carbon (BC), sulfate (SO 4 2- ), nitrate (NO 3 - ), ammonium (NH 4 + ), and soil dust (Dust)]. The neurodevelopment of children was assessed using Bayley-III Screening Test. After adjusting for confounding factors, the risk of non-optimal gross motor development increased by 31 % for every 10 μg/m 3 increase in average PM 2.5 exposure during gestation (aRR: 1.31; 95 % CI: 1.04, 1.64). Further analysis of PM 2.5 constituents showed that prenatally exposed to high SO 4 2- was associated with the risk of non-optimal gross motor development (aRR: 1.40; 95 % CI: 1.08, 1.81). Null associations were observed for the rest four neurodevelopment domains. Collectively, our study suggested that prenatal exposure to PM 2.5 , particularly with high SO 4 2- concentration, was associated with children's non-optimal gross motor development at 1 year old. The short- and long-term influences of perinatal PM 2.5 exposure on children's neurodevelopment warrant further investigation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Fifteen undescribed dimeric sesquiterpenoids, linderanoids A-O along with one known lindenane-type sesquiterpenoid dimer, lindenaneolide F, were isolated and identified from the roots of Lindera aggregata. Their structures and absolute configurations were elucidated using spectroscopy and electronic circular dichroism (ECD) analysis. All the isolated compounds were screened for transforming growth factor (TGF)-β inhibitory activity, and the results showed that linderanoid E significantly inhibited the TGF- β induced smad2 phosphorylation at a concentration of 25 μM., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Breast cancer (BRCA) is one of the most threatening cancer types, especially among the female population. 70% of breast cancer are estrogen receptor α (ERα) positive and endocrine therapy is effective to decrease breast cancer risk. Autophagy, a highly conserved cellular recycling process, has been regarded to serve a protective role in BRCA. Autophagy-related gene 13 (Atg13) is participated in autophagy and is critical to autophagy initiation. Briefly, we observed that ERα, a well-known transcription factor that can promote breast cancer cell proliferation, expressed higher in breast cancer tissues. Moreover, ERα had a significant positive correlation with Atg13 and may be able to regulate the transcription of Atg13 via binding the promoter region of Atg13. Surprisingly, Oxabicycloheptene sulfonate (OBHS), the drug that we reported as a selective estrogen receptor modulator (SERM) before, may have the ability to decrease the expression of ERα and suppress the autophagy. In conclusion. We found that ERα could be involved in autophagy by binding the promoter of Atg13, and compound OBHS may be able to affect the viability of breast cancer cells by decreasing the expression of ERα and Atg13., Competing Interests: Declaration of competing interest I would like to declare that the work described was original that has not been published previously, and not under consideration for publication elsewhere, in whole or in part. All the authors listed have approved the manuscript that is enclosed. No conflict of interest exists in the submission of this manuscript, and the manuscript is approved by all authors for publication., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Co-pyrolysis of sewage sludge and straws has been used to improve the pore structure and reduce the ecological risks of heavy metals in sewage sludge-derived biochars. However, to date, no study has focused on the effects of biochar derived from sewage sludge/straws on the immobilization and phytoavailability of heavy metals in soil. Here, we studied the effects of biochar derived from sewage sludge/cotton stalks (SCB) and that derived from sewage sludge alone (SSB) on the remediation of sandy loam soil contaminated by Pb, Cu, and Zn. SCB amendment decreased the bioavailable forms of Pb, Cu, and Zn in the soil by 19.0%, 34.9%, and 18.2%, respectively, and reduced their accumulation in ryegrass by 28.6%, 50.1%, and 30.0%, respectively, compared with those by SSB amendment. Furthermore, SCB amendment transformed more metals from the acid-soluble fraction to the oxidizable fraction than SSB amendment, indicating that complexation played a more critical role in SCB amendment than in SSB amendment. Both biochar amendments effectively improved soil water holding capacity, increased the supply of available P, N, and K, and promoted ryegrass growth. The findings of this study show the benefits of SCB over SSB for the remediation of heavy metal-contaminated soil., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Background: Osteosarcoma is the most common primary malignant bone tumor, particularly among children and adolescents, and the prognosis of osteosarcoma patients remains poor. The NADPH oxidase 2 (NOX2) has been found over-expressed in several human cancers, and closely associated with poor prognosis. Meanwhile the role of NOX2 in osteosarcoma patients has not been reported. This study aimed to investigate the clinicopathological and prognostic significance of NOX2 in osteosarcoma patients., Methods: Immunohistochemistry (IHC), western blot (WB) and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) were used to detect the expression of NOX2 in 55 primary osteosarcoma specimens and in 20 non-neoplastic bone tissue specimens. The correlations between NOX2 expression and clinicopathological parameters were analysed by using the χ2 test or Fisher's exact test. Disease free survival and overall survival of osteosarcoma patients were assessed by using the Kaplan-Meier method and Cox proportional hazards model., Results: NOX2 was over-expressed significantly in osteosarcoma compared with that in non-neoplastic bone tissue, and correlated with progression free survival (P < 0.001) and overall survival (P < 0.001). The over-expression of NOX2 was associated with tumor size (P < 0.001), tumor location (P < 0.001). The Cox analysed shown that the over-expression of NOX2 was predicted to be worse PFS (hazard ratio (HR) = 4.10, P = 0.004) and OS (hazard ratio (HR) = 3.50, P = 0.010) time in osteosarcoma patients., Conclusions: The results of our study suggest that the over-expression of NOX2 is related to adverse clinical outcome, and can be viewed as an independent prognostic marker in osteosarcoma. Further research is required to verify the predictive value of NOX2 in osteosarcoma patients., Competing Interests: Declaration of Competing Interest None of the authors have any conflict of interest., (Copyright © 2020 The Japanese Orthopaedic Association. Published by Elsevier B.V. All rights reserved.)

Background: Therapeutic products with coagulation factor VIII (FVIII) have a wide range of specific activities, implying presence of protein with altered structure. Previous studies showed that recombinant FVIII products (rFVIII) contain a fraction (FVIII FT ) unable to bind von Willebrand factor (VWF) and reported to lack activity. Because of loss of function(s), FVIII FT can be defined as a product-related impurity, whose properties and levels in rFVIII products should be investigated., Objective: To isolate and characterize the FVIII FT fraction in rFVIII products., Methods: Protein fractions unable (FVIII FT ) and able (FVIII EL ) to bind VWF were isolated from rFVIII products using immobilized VWF affinity chromatography (IVAC) and characterized by gel electrophoresis, immunoblotting, FVIII activity test, surface plasmon resonance, mass spectrometry, and for plasma clearance in mice., Results and Conclusions: A robust IVAC methodology was developed and applied for analysis of 10 rFVIII products marketed in the United States. FVIII FT was found at various contents (0.4%-21.5%) in all products. Compared with FVIII EL , FVIII FT had similar patterns of polypeptide bands by gel electrophoresis, but lower functional activity. In several representative products, FVIII FT was found to have reduced sulfation at Tyr1680, important for VWF binding, decreased interaction with a low-density lipoprotein receptor-related protein 1 fragment, and faster plasma clearance in mice. These findings provide basic characterization of FVIII FT and demonstrate a potential for IVAC to control this impurity in rFVIII products to improve their efficacy in therapy of hemophilia A., (Published 2021. This article is a U.S. Government work and is in the public domain in the USA.)

Background: Driveline infections remain a major complication of ventricular assist device (VAD) implantation. This study aimed to characterize in vivo microbial biofilms associated with driveline infections and host tissue integration of implanted drivelines., Methods: A total of 9 infected and 13 uninfected drivelines were obtained from patients with VAD undergoing heart transplantation in Australia between 2016 and 2018. Each driveline was sectioned into 11 pieces of 1.5 cm in length, and each section was examined by scanning electron microscopy (SEM) and viable counts for microbial biofilms. Microorganisms were cultured and identified. Host tissue integration of clinical drivelines was assessed with micro-computed tomography (CT) and SEM. An in vitro interstitial biofilm assay was used to simulate biofilm migration in the driveline tunnel, and time-lapse microscopy was performed., Results: Of the 9 explanted, infected drivelines, all had organisms isolated from varying depths along the velour section of the drivelines, and all were consistent with the swab culture results of the clinically infected exit site. SEM and micro-CT suggested insufficient tissue integration throughout the driveline velour, with microgaps observed. Clinical biofilms presented as microcolonies within the driveline tunnel, with human tissue as the sub-stratum, and were resistant to anti-microbial treatment. Biofilm migration mediated by a dispersal-seeding mechanism was observed., Conclusions: This study of explanted infected drivelines showed extensive anti-microbial-resistant biofilms along the velour, associated with microgaps between the driveline and the surrounding tissue. These data support the enhancement of tissue integration into the velour as a potential preventive strategy against driveline infections by preventing biofilm migration that may use microgaps as mediators., (Copyright © 2020 International Society for Heart and Lung Transplantation. Published by Elsevier Inc. All rights reserved.)

Presbycusis is a form of age-related hearing loss (AHL). Many studies have shown that the degeneration of various structures in the cochlea of the inner ear is related to AHL, and DNA damage is an important factor leading to the above process. As an E2 ubiquitin-conjugated enzyme, RAD6B plays an important role in DNA damage repair (DDR) through histone ubiquitination. However, the molecular mechanism is still unclear. In this study, we investigated the role of RAD6B in the morphological changes and DDR mechanisms in aging-related degeneration of the cochlea of mice. We observed that the hair cells, stria vascularis and spiral ganglion in the cochlea of the RAD6B knockout mice showed significant degenerative changes and abnormal expression of proteins associated with DDR mechanisms compared with those of the littermate wild-type mice. In conclusion, our results suggest that the deletion of RAD6B may lead to abnormalities in DDR, thereby accelerating the degeneration of various structures in the cochlea and senescence and apoptosis of cochlea cells., Competing Interests: Declaration of competing interest All authors declare that they have no conflicts of interest., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Xiaokewan is a typical Traditional Chinese medicine (TCM) for diabetes and contains various natural chemicals, such as lignans, flavonoids, saponins, polysaccharides, and western medicine glibenclamide. In the current study, a highly efficient system for screening hypoglycemic efficacy constituents of Xiaokewan has been developed with the integration of intelligent data acquisition, data mining, network pharmacology, and computer assisted target fishing. With the combination of background exclusion data dependent acquisition (BE-DDA) and non-targeted precise-and-thorough background-subtraction (PATBS) techniques, a novel workflow has been established for the non-targeted recognition and identification of TCM constituents in vivo, and has been applied to the exposure study of Xiaokewan in rat. In this case, an interesting correlation among drug, target, and disease can be established, by combining the screening or characterization results with the strategy of network pharmacology and multiple computer assisted techniques. Consequently, five main constituents (puerarin, daidzein, formononetin, deoxyschizandrin and glibenclamide) exposed in vivo have been selected as effective hypoglycemic components. Meanwhile, the network pharmacology experimental results showed that these five constituents could act on various drug targets, such as PI3K, PTP1B, MAPK, AKT, TNF, and NF-κB. These five constituents might be involved in the regulation of β-cell function or exhibit inflammation inhibition ability to relieve the pathophysiological process of disease from multiple links. Furthermore, the pharmacological effects of these five constituents have been verified by diabetic zebrafish model. The zebrafish model results showed that the TCM monomer mixture without glibenclamide exhibited similar hypoglycemic activity with Xiaokewan. Although the monomer mixture with glibenclamide showed better activity than Xiaokewan only, the deoxyschizandrin (TCM constituent of Xiaokewan) exhibited best hypoglycemic performance. In summary, the above results indicated that the application of both intelligent recognition technology in mass spectrometry dataset and computerized network pharmacology might provide a pioneering approach for investigating the substance basis of TCM and searching lead compounds from natural sources., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

The powder-based photocatalytic material is often difficult on wide application and then loaded on a matrix for separating conveniently from the liquid. Submerged photocatalysts may not take advantage of the light energy adequately. Thus, this boundedness may reduce their utilization and potentially cause the secondary pollution on the environment. In this paper, the micron-sized silica sphere is used as a floating substrate, and the visible-light-driven photocatalytic material iodine oxygen bismuth is prepared onto the hollow silica microspheres. The composite spheres as the visible-light-driven photocatalytic material have been characterized by XPS, XRD, SEM, EDX, PL, etc. It confirmed that BiOI combined on the SiO 2 microsphere (mSiO 2 ) by Bi-O-Si. The photogenerated electrons of the composite have a low probability of recombination and have a narrow band energy (1.82 eV). The composite was used to photodegrade diesel-containing wastewater and rhodamine B, and the superoxide group (·O 2 - ) was found to be the main degradation active factor. And by GC-MS test, it is known that the superoxide group (·O 2 - ) can degrade long-chain alkanes into short chains or form branches. Detailed studies on the acute exposure experiments of Vibrio qinghaiensis sp.-Q67 and zebrafish embryos showed that the composites can effectively reduce the toxicity of BiOI and mSiO 2 ., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Stress-induced gastric ulcer is one of the common complications affecting patients after trauma, mainly leading to gastrointestinal bleeding and perforation, and severe cases may be life-threatening. However, the molecular mechanism of stress-induced gastric ulcer remains unclear. In the present study, RNA-sequencing was performed on gastric tissues of normal rats (C), stress-induced gastric ulcer rats (T0), and rats recovered from gastric ulcer for 3 days (T3), and bioinformatics analysis was performed to determine changes in gene expression and biological pathways. The protein-protein interaction (PPI) networks of differentially expressed genes (DEGs) were constructed by STRING and visualized by the Cytoscape software. The associated transcriptional factor (TFs)-gene regulatory network of the hub DEGs was also constructed. Pairwise comparisons obtained 103 (T0&#95;C), 127 (T3&#95;T0), and 13 (T3&#95;C) DEGs, respectively. Gene ontology (GO) enrichment analysis indicated DEGs in T0&#95;C and T3&#95;T0 were significantly enriched in response to oxygen-containing compound, response to organic substance, and response to external stimulus. Pathway analysis suggested that DEGs were enriched in TNF signaling pathway, PPAR signaling pathway, apoptosis, and IL-17 signaling pathway. Seven hub genes (Fos, Jun, Nfkbia, Dusp1, Pim3, Junb, and Fosb) were obtained from the PPI networks of T0&#95;C and T3&#95;T0. Key TFs with close interactions, such as Fos, Jun, Nfkbia, Junb, Egr1, and Fosb, were screened This study used RNA-sequencing and bioinformatics analysis to screen out genes associated with gastric ulcer, which can help reveal the molecular mechanism of gastric ulcer development and restoration, and provide reference for the treatment of human gastric ulcers.

Heavy metal pollution has become an important issue threatening human health and the liver is a very important metabolic organ. Here, we use label-free Raman confocal imaging to study the alterations of the liver tissue after cadmium pollution. Raman imaging has been performed on 100μmx100μm liver tissues to study the distribution of important macromolecules and the average Raman spectrum of the entire region has been used to characterize and quantize the change of biochemical compositions in liver tissue. The poisoned livers displayed a significant decrease in the intensity of 748 cm -1 , 1128 cm -1 and 1585 cm -1 bands of cytochrome C, in comparison to the control. The collagen peak at 1082 cm -1 is significantly higher than that of control, suggesting the increasing fibrosis of Cd liver tissues. To confirm the results, we selected a 30μmx15μm liver cell area for high-resolution Raman imaging. We observed a substantial increase of lipids and proteins at specific points of hepatocytes. The confocal Raman imaging of liver tissues provided a unique tool to better understand disease-induced changes in the biochemical phenotype of primary liver tissues. Our study provides valuable references as in vitro models for studying Cd accumulation and toxicity in human liver., (Copyright © 2019. Published by Elsevier B.V.)

Objective: We aimed to estimate the risk of preeclampsia (PE) associated with in vitro fertilization (IVF) and potential predisposing factors responsible for the observed association., Methods: This retrospective cohort study included 114485 pregnant women who delivered at the Nanjing Maternity and Child Health Care Hospital between 2013 and 2018. Of the 114485 women, 4601 (4%) conceived through IVF (IVF group) and 109884 (96%) conceived spontaneously (SC group). We performed logistic regression analysis to evaluate the risk of PE following IVF compared to spontaneous conception (SC). Then, we used propensity score matching analysis to compare the clinical characteristics and pregnancy outcomes between IVF patients with and without PE., Result: There were 1339 PE cases in the total study population, with a significantly higher incidence of PE in IVF relative to spontaneous pregnancies (6.1% vs. 1.0%, p < 0.01). Severe PE was more prevalent in singleton IVF-PE group than in singleton SC-PE group (40% vs. 24.1%, p = 0.025). Placenta accreta was more common in singleton preeclamptic patients with IVF than without IVF (12.5vs.2.6%, p = 0.003). Placental hypoxia was more prevalent in twin IVF pregnancies with PE than without PE (6% vs. 12.2%, p = 0.045). Moreover, the IVF-PE group showed more frequent first-trimester bleeding (31.6% vs. 10.5%, p = 0.024) compared to the control group., Conclusion: IVF is associated with the onset and progression of PE. Defective placentation and placental insufficiency may predispose IVF patients to PE and may manifest as first-trimester bleeding., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: With the development of next-generation sequencing (NGS), thousands of circular RNAs (circRNAs) have been found. Many circRNAs have been verified to play vital roles in carcinogenesis. However, whether circRNAs engage in the development and progression of ovarian cancer remains to be clarified., Methods: We analyzed circRNA expression profiling in epithelial ovarian cancer (EOC) and normal ovarian tissues (NOT) using NGS and validated six randomly selected circRNAs via quantitative real-time-PCR (qRT-PCR), reverse-transcription PCR (RT-PCR) and Sanger sequencing after RNase treatment. CircHIPK3, the most abundant circRNA in our sequencing data, was further knocked down by siRNA. The circHIPK3 function in proliferation, invasion, migration and apoptosis of ovarian cancer cells and normal ovarian epithelial cells was analyzed via cell counting-kit 8 (CCK8), wound healing, transwell and flow cytometry analyses after circHIPK3 was efficiently silenced., Results: Altogether, we found 7333 circRNAs, of which 4505 (61.43%) were newly identified, 2431 were significantly upregulated and 3120 were remarkably downregulated. Six randomly selected differentially expressed circRNAs were examined in 18 EOC and 18 NOT. Furthermore, the results of RT-PCR and Sanger sequencing after RNase treatment confirmed head-to-tail back-splicing. Silencing of circHIPK3 promoted proliferation, migration, and invasion and inhibited apoptosis of ovarian cancer cells (A2780 and SKOV3) and normal ovarian epithelial cells (IOSE80). Additionally, the circHIPK3-miRNA-mRNA axis was predicted as the possible mechanism using bioinformatic approaches., Conclusions: We identified the circRNA expression profile in ovarian cancer tissues and further verified the existence and expression of six randomly selected differentially expressed circRNAs. Besides, we also found that circHIPK3 is an important regulator of ovarian cancer progression., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Early-onset preeclampsia (EOPE), which is the most severe form of the syndrome, confers a high risk of neonatal morbidity and perinatal death. We aim to study the roles of long non-coding RNAs (lncRNAs) in the pathogenesis of early-onset preeclampsia (EOPE). Therefore, we examined the expression profiles of lncRNAs between early-onset preeclampsia and preterm controls using microarray analysis. Quantitative real-time PCR (qRT-PCR) was performed to verify the selected differentially expressed lncRNAs. In total, we identified 15,646 upregulated and 13,178 downregulated lncRNAs in the placenta of EOPE patients compared to the preterm controls. Gene ontology and pathway analysis revealed that compared to the preterm controls, many of the processes over-represented in the EOPE patients were related to cell migration and cell motility. A selection of the differentially expressed lncRNA transcripts was confirmed using qRT-PCR, particularly RP11-465L10.10, which is associated with the MMP9 gene. These data may offer a background/reference resource for future functional studies of lncRNAs related to EOPE., (Copyright © 2016 Elsevier B.V. All rights reserved.)

The composition of major hexabromocyclododecane (HBCD) diastereoisomers, i.e. α-, β-, and γ-HBCDs, in marine biota is different from that of the commercially available form (technical HBCD), which is used extensively for toxicological studies. To properly evaluate the impact of HBCDs, the embryos of Oryzias melastigma were used to examine the developmental toxicity of the individual diastereoisomers. Results showed that HBCD diastereoisomers at the environmentally realistic concentrations in the embryos induced malformation rate and heartbeat, and caused the appearance of apoptotic heart. In addition, α-, β-, and γ-HBCDs had similar potency to stimulate the generation of reactive oxygen species, consequently leading to apoptosis in O. melastigma embryos. The order of the developmental toxicity of α-, β-, and γ-HBCDs in O. melastigma embryos was different from that in zebrafish embryos studied previously, which highlighted the importance of using species from both fresh and salt water for toxicity assessment., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

A novel coumarin-based fluorescent probe L ((4E)-4-((7-hydroxy-4-methyl-2-oxo-2H-chromen-8-yl) methyleneamino)-1,2-dihyydro-2,3-dimethyl-1-phenylpyrazol-5-one) has been developed as a simple and efficient chemosensor which exhibits a significant fluorescence reduction in the presence of metal cations. This sensor exhibits high selectivity and sensitivity toward Cu(2+) over other common cations. The mechanism for detecting copper was evaluated by time-dependent density functional theory (TD-DFT) calculations and the coordination mode was also confirmed by density functional theory (DFT) calculations. Furthermore, results of cell imaging in this study indicate that this new probe may be useful for detection and monitoring of Cu(2+) in biological applications., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Accurate and reliable quantitative proteomics in cell culture has been considerably facilitated by the introduction of the stable isotope labeling by amino acids in cell culture (SILAC), combined with high resolution mass spectrometry. There are however several major sources of quantification errors that commonly occur with SILAC techniques, i.e. incomplete incorporation of isotopic amino acids, arginine-to-proline conversion, and experimental errors in final sample mixing. Dataset normalization is a widely adopted solution to such errors, however this may not completely prevent introducing incorrect expression ratios. Here we demonstrate that a label-swap replication of SILAC experiments was able to effectively correct experimental errors by averaging ratios measured in individual replicates using quantitative proteomics and phosphoproteomics of ligand treatment of neural cell cultures. Furthermore, this strategy was successfully applied to a SILAC triplet experiment, which presents a much more complicated experimental matrix, affected by both incomplete labeling and arginine-to-proline conversion. Based on our results, we suggest that SILAC experiments should be designed to incorporate label-swap replications for enhanced reliability in expression ratios., (Published by Elsevier B.V.)

In this study, a spectral probing method was applied to determine the content of the main components, i.e., proteins, polysaccharides and humic substances, in the extracellular polymeric substances (EPS) extracted from activated sludge. The measurement results were consistent with those obtained from the conventional methods, such as the anthrone for polysaccharide determination, the modified Lowry method for protein and humic substance determination. The recoveries for the determination of proteins, humic substances and polysaccharides in the EPS extracted from six sludge samples using standard additional method were between 92.4 and 108.9%, 84.8 and 108.9%, 75.1 and 117.2%, respectively. These results indicate that the propose method has a good accuracy and precision, and can be used as an effective approach to determine the main components in sludge EPS., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Pulsed Q collision-induced dissociation (PQD) was developed in part to facilitate detection of low-mass reporter ions using labeling reagents (e.g. iTRAQ) on LTQ platforms. It has generally been recognized that the scan speed and sensitivity of an LTQ are superior than those of an Orbitrap using the higher-energy collisional dissociation (HCD). However, the use of PQD in quantitative proteomics is limited, primarily due to the meager reproducibility of reporter ion ratios. Optimizations of PQD for iTRAQ quantification using LTQ have been reported, but a universally applicable strategy for quantifying the less abundant proteins has not been fully established. Adjustments of the AGC target, μscan, or scan speed offer only incremental improvements in reproducibility. From our experience, however, satisfactory coefficients of variation (CVs) of reporter ion ratios were difficult to achieve using the discovery-based approach. As an alternative, we implemented a target-based approach that obviates data dependency to allow repetitive data acquisitions across chromatographic peaks. Such a strategy generates enough data points for more reliable quantification. Using cAMP treatment in S49 cell lysates and this target-based approach, we were able to validate differentially expressed proteins, which were initially identified as potential candidates using the discovery-based PQD. The target-based strategy also yielded results comparable to those obtained from HCD in an Orbitrap. Our findings should aid LTQ users who desire to explore iTRAQ quantitative proteomics but have limited access to the more costly Orbitrap or other instruments., (Published by Elsevier B.V.)

The EIAV (equine infectious anemia virus) multi-species attenuated vaccine EIAV(DLV121) successfully prevented the spread of equine infectious anemia (EIA) in China in the 1970s and provided an excellent model for the study of protective immunity to lentiviruses. In this study, we compared immune responses induced by EIAV(DLV121) to immunity elicited by the virulent EIAV(LN40) strain and correlated immune responses to protection from infection. Horses were randomly grouped and inoculated with either EIAV(DLV121) (Vaccinees, Vac) or a sublethal dose of EIAV(LN40) (asymptomatic carriers, Car). Car horses became EIAV(LN40) carriers without disease symptoms. Two of the four Vac horses were protected against infection and the other two had delayed onset or reduced severity of EIA with a lethal EIAV(LN40) challenge 5.5 months post initial inoculation. In contrast, all three Car animals developed acute EIA and two succumbed to death. Specific humoral and cellular immune responses in both Vac and Car groups were evaluated for potential correlations with protection. These analyses revealed that although plasma viral loads remained between 10(3) and 10(5)copies/ml for both groups before EIAV(LN40) challenge, Vac-treated animals developed significantly higher levels of conformational dependent, Env-specific antibody, neutralizing antibody as well as significantly elevated CD4(+) T cell proliferation and IFN-γ-secreting CD8(+) T cells than those observed in EIAV(LN40) asymptomatic carriers. Further analysis of protected and unprotected cases in vaccinated horses identified that cellular response parameters and the reciprocal anti-p26-specific antibody titers closely correlated with protection against infection with the pathogenic EIAV(LN40). These data provide a better understanding of protective immunity to lentiviruses., (Copyright © 2011 Elsevier B.V. All rights reserved.)

We have created a novel enzyme reactor using electric field-mediated orientation and immobilization of proteolytic enzymes (trypsin/chymotrypsin) on biocompatible PVDF membranes in a continuous flow-through chamber. Using less than 5min, this reactor in various enzyme combinations can produce enhanced rapid digestion for standardized prototypic proteins, hydrophilic proteins and hydrophobic transmembrane proteins when compared to in-solution techniques. With improved digestive efficiency, our reactor improved the overall functional analysis of lipid raft proteomes by identifying more closely functionally linked proteins and elucidated a richer set of biological processes and pathways linked to the proteins than traditional in-solution methods., (Published by Elsevier B.V.)

FAT10, also known as diubiquitin, has been implicated in the regulation of diverse cellular processes, including mitosis, immune response, and apoptosis. We seek to identify FAT10-targeted proteins, an essential step in elucidating the physiological function of FAT10. To this end, human FAT10 or its non-conjugatable derivative, FAT10ΔGG, was overexpressed in HEK293 cells. We observed a number of high molecular weight FAT10 conjugates in cells expressing wild-type FAT10, but not in FAT10ΔGG. The FAT10 conjugates are inducible by TNF-α and accumulated significantly when cells were treated with proteasome inhibitor, MG132. Among them, tumor suppressor p53 was found to be FATylated. The p53 transcriptional activity was found to be substantially enhanced in FAT10-overexpressing cells. In addition, overexpressing FAT10 in HEK293 cells also reduced the population of p53 which cross reacted with monoclonal anti-p53 antibody, PAB240, known to recognize only the transcriptionally inactive p53. FAT10 in the nucleus was found co-localized with p53 and altered its subcellular compartmentalization. Furthermore, overexpressing FAT10 led to a reduction in the size of promyelocytic leukemia nuclear bodies (PML-NBs) and altered their distribution in the nucleus. Based on these observations, a potential mechanism which correlates FATylation of p53 to its translocation and transcriptional activation is discussed., (Copyright © 2011. Published by Elsevier Inc.)

Pulmonary arterial hypertension (PAH) is emerging as a major complication and independent risk factor for death among adults with sickle cell disease (SCD). Using surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF MS), we searched for biomarkers of PAH in plasma specimens from 27 homozygous sickle cell anemia (HbSS) patients with PAH and 28 without PAH. In PAH patients, analysis consistently showed lower abundance of a 28.1-kDa peak (P < .001), identified by high-resolution mass spectrometry as the oxidant-scavenging protein apolipoprotein A-I (apoA-I), which correlated with clinical assays of apoA-I (r = .58, P < .001) and high-density lipoprotein (HDL) levels (r = .50, P = .001). Consistent with endothelial dysfunction that may mediate this effect in PAH, HbSS patients with lower apoA-I levels also displayed impaired vasodilatory responses to acetylcholine (mean +/- SEM, 189% +/- 34% [n = 13] vs 339% +/- 51% [n = 13], P < .001). As a group, patients with SCD demonstrated significantly lower apoA-I levels than African-American control subjects. The PAH cohort was further characterized by high levels of apolipoproteins A-II and B and serum amyloid A, and low levels of haptoglobin dimers and plasminogen. These results imply a relationship of apolipoproteins to the development of PAH vasculopathy in SCD, potentially involving an unexpected mechanistic parallel to atherosclerosis, another proliferative vasculopathy.

Exosomes are nanovesicles that are released from cells as a mechanism of cell-free intercellular communication. Only a limited number of proteins have been identified from the plasma exosome proteome. Here, we developed a multi-step fractionation scheme incorporating gel exclusion chromatography, rate zonal centrifugation through continuous sucrose gradients, and high-speed centrifugation to purify exosomes from human plasma. Exosome-associated proteins were separated by SDS-PAGE and 66 proteins were identified by LC-MS/MS, which included both cellular and extracellular proteins. Furthermore, we identified and characterized peroxisome proliferator-activated receptor-gamma (PPARgamma), a nuclear receptor that regulates adipocyte differentiation and proliferation, as well as immune and inflammatory cell functions, as a novel component of plasma-derived exosomes. Given the important role of exosomes as intercellular messengers, the discovery of PPARgamma as a component of human plasma exosomes identifies a potential new pathway for the paracrine transfer of nuclear receptors.

Chemical modification of proteins is often carried out to generate protein-small molecule conjugates for various applications. The high resolution and mass accuracy of a Fourier transform mass spectrometer is particularly useful for assessing the extent or sites of covalent modifications. As protein-small molecule reactions often produce products with variable numbers of the compound incorporated at different sites, a direct mass analysis of the reaction products at times yields mass spectra hard to interpret. Chromatographic separation at protein level could reduce the complexity of a sample, thus allowing more accurate mass spectrometric analysis. In this report, we demonstrate the utility of reversed-phase protein chromatography and FT-ICR mass spectrometry in analyzing CCNU (lomustine, 1-(2-chloroethyl)-3-cyclohexyl-1-nitroso-urea, MW: 233.7Da) modification of stathmin. With this combined approach, we determined the stoichiometry as well as sites of CCNU incorporation into the protein, demonstrating differential reactivity of several lysyl residues to CCNU alkylation.

A sensitive and specific method was developed and validated for the determination of paeoniflorin in rat brain with liquid chromatography-tandem mass spectrometry. Sample pretreatment involved protein precipitation following solid-phase extraction. Paeoniflorin and geniposide (internal standard) were separated isocratically on a Waters Symmetry C18 column (150 mm x 2.1 mm i.d., 5 microm), using a mobile phase of methanol/water with 0.1% formic acid (50:50, v/v) at a flow-rate of 200-300 microL/min in 4min. A Finngan LTQ tandem mass spectrometer equipped with electrospray ionization source was operated in the positive ion mode. Selective reaction monitoring was performed to quantify paeoniflorin and the internal standard at m/z transitions of 503-->381 and 411-->231, respectively. A good linearity was found in the range of 2-500 ng/mL (R(2)=0.9939). The intra- and inter-batch assay precisions (coefficient of variation, CV) at 5, 50 and 400 ng/mL (n=5) ranged from 6.3% to 9.7% and 1.2% to 7.2%, respectively, and the accuracies were from 95.9% to 101.6% and 99.4% to 102.9%, respectively. The mean recoveries of paeoniflorin were 81.2%, 80.9% and 82.3% at 5, 50 and 400 ng/mL (n=5), respectively, and the mean recovery of the internal standard was 76.7% with a concentration of 50 ng/mL (n=5). Stability studies showed that paeoniflorin was stable in different conditions. Finally, the method was successfully applied to the pharmacokinetic study of paeoniflorin in rat brain following a single subcutaneous administration (10 mg/kg) to rats.

Ubiquitin-like modifiers (UBLs) contain ubiquitin homology domains and can covalently modify target proteins in a manner similar to ubiquitylation. In this study, we revealed a general proteomic approach to elucidate the enzymatic pathways and identify target proteins for three UBLs: SUMO-2, SUMO-3, and NEDD8. Expression plasmids containing the cDNAs of Myc/6xHis doubly-tagged processed or non-conjugatable forms of these UBLs were constructed. The constructed vectors were then used to transfect HEK 293 Tet-On cells, and stable cell lines expressing these UBLs and their mutants were established. The epitope-tagged proteins were purified by immunoprecipitation under native conditions or by affinity chromatography on nickel resin under denaturing conditions. Purified proteins were analyzed using liquid chromatography coupled with mass spectrometry (LC-MS/MS). Most of the E1-like activating enzymes, E2-like conjugating enzymes and the majorities of the known target as well as some previously unreported proteins for SUMO-2, SUMO-3, and NEDD8 pathways were identified.

High-density lipoproteins (HDL) were examined as potential carriers of small peptides in plasma. HDL purified by density gradient centrifugation was delipidated and fractionated by size-exclusion chromatography under denaturing conditions. By HPLC and mass spectrometry, more than 100 peptide components were found in the size range from 1000 to 5000 Da. By sequence analysis, peptides were identified as fragments of proteins such as apolipoproteins, fibrinogen, alpha1-proteinase inhibitor, and transthyretin. The results indicate that purified HDL bears a complex range of small peptides. It is unclear whether the peptides have any significant functional role as apolipopeptides, but they may represent a pathway for peptide delivery or scavenging and a significant reservoir of plasma peptides for diagnostic evaluation.