76
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Dong H, Wang M, Fan S, Wu C, Zhang C, Wu X, Xue B, Cao Y, Deng J, Yuan D, Shi J. Redox‐Regulated Conformational Change of Disulfide‐Rich Assembling Peptides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202212829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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77
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Guo Y, Li Q, Ren W, Wu H, Wang C, Li X, Xue B, Qiu Y, Zhang J, Chen J, Fang L. Quantitative Proteomics Reveals Down-Regulated Glycolysis/Gluconeogenesis in the Large-Duct Type Intrahepatic Cholangiocarcinoma. J Proteome Res 2022; 21:2504-2514. [PMID: 36066509 DOI: 10.1021/acs.jproteome.2c00472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is a lethal hepatobiliary malignancy that arises from the epithelial cells of the intrahepatic bile ducts, accounting for approximately 10% of cholangiocarcinoma (CCA). According to the 2019 World Health Organization (WHO) classification of tumors of the digestive system, iCCA is divided into small-duct type (SD-type) and large-duct type (LD-type). However, it remains unknown which molecular events contribute to the disparity. To explore the proteomic characteristics of iCCA, we used an isobaric tag for relative and absolute quantitation (iTRAQ) based quantitative proteomics strategy to investigate stably dysregulated proteins in the SD-type and LD-type of iCCA tissues. Importantly, we found three glycolysis/gluconeogenesis-related enzymes, triosephosphate isomerize 1 (TPI1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and phosphoglycerate kinase 1 (PGK1), were significantly down-regulated in the LD-type iCCA, which were further confirmed by immunohistochemistry using tissue microarray. Moreover, we demonstrated that the knockdown of these three candidate proteins by siRNAs notably increased the ability of proliferation in two CCA cell lines (HuH28 and RBE), suggesting that effective down-regulation of the glycolysis/gluconeogenesis pathway might be an underlying novel mechanism contributing to the LD-type iCCA.
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Bashir Z, Yu W, Xu Z, Li Y, Lai J, Li Y, Cao Y, Xue B. Engineering Bio-Adhesives Based on Protein–Polysaccharide Phase Separation. Int J Mol Sci 2022; 23:ijms23179987. [PMID: 36077375 PMCID: PMC9456018 DOI: 10.3390/ijms23179987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Glue-type bio-adhesives are in high demand for many applications, including hemostasis, wound closure, and integration of bioelectronic devices, due to their injectable ability and in situ adhesion. However, most glue-type bio-adhesives cannot be used for short-term tissue adhesion due to their weak instant cohesion. Here, we show a novel glue-type bio-adhesive based on the phase separation of proteins and polysaccharides by functionalizing polysaccharides with dopa. The bio-adhesive exhibits increased adhesion performance and enhanced phase separation behaviors. Because of the cohesion from phase separation and adhesion from dopa, the bio-adhesive shows excellent instant and long-term adhesion performance for both organic and inorganic substrates. The long-term adhesion strength of the bio-glue on wet tissues reached 1.48 MPa (shear strength), while the interfacial toughness reached ~880 J m−2. Due to the unique phase separation behaviors, the bio-glue can even work normally in aqueous environments. At last, the feasibility of this glue-type bio-adhesive in the adhesion of various visceral tissues in vitro was demonstrated to have excellent biocompatibility. Given the convenience of application, biocompatibility, and robust bio-adhesion, we anticipate the bio-glue may find broad biomedical and clinical applications.
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Dai J, Zhang G, Alkhofash RA, Mekonnen B, Saravanan S, Xue B, Fan ZC, Betleja E, Cole DG, Liu P, Lechtreck K. Loss of ARL13 impedes BBSome-dependent cargo export from Chlamydomonas cilia. J Cell Biol 2022; 221:213429. [PMID: 36040375 PMCID: PMC9436004 DOI: 10.1083/jcb.202201050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/12/2022] [Accepted: 07/11/2022] [Indexed: 12/25/2022] Open
Abstract
The GTPase Arl13b participates in ciliary protein transport, but its contribution to intraflagellar transport (IFT), the main motor-based protein shuttle of cilia, remains largely unknown. Chlamydomonas arl13 mutant cilia were characterized by both abnormal reduction and accumulation of select membrane-associated proteins. With respect to the latter, a similar set of proteins including phospholipase D (PLD) also accumulated in BBSome-deficient cilia. IFT and BBSome traffic were apparently normal in arl13. However, transport of PLD, which in control cells moves by BBSome-dependent IFT, was impaired in arl13, causing PLD to accumulate in cilia. ARL13 only rarely and transiently traveled by IFT, indicating that it is not a co-migrating adapter securing PLD to IFT trains. In conclusion, the loss of Chlamydomonas ARL13 impedes BBSome-dependent protein transport, resulting in overlapping biochemical defects in arl13 and bbs mutant cilia.
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80
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Li SJ, Zhang G, Xue B, Ding Q, Han L, Huang JC, Wu F, Li C, Yang C. Toxicity and detoxification of T-2 toxin in poultry. Food Chem Toxicol 2022; 169:113392. [PMID: 36044934 DOI: 10.1016/j.fct.2022.113392] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/14/2022] [Accepted: 08/23/2022] [Indexed: 11/27/2022]
Abstract
This review summarizes the updated knowledge on the toxicity of T-2 on poultry, followed by potential strategies for detoxification of T-2 in poultry diet. The toxic effects of T-2 on poultry include cytotoxicity, genotoxicity, metabolism modulation, immunotoxicity, hepatotoxicity, gastrointestinal toxicity, skeletal toxicity, nephrotoxicity, reproductive toxicity, neurotoxicity, etc. Cytotoxicity is the primary toxicity of T-2, characterized by inhibiting protein and nucleic acid synthesis, altering the cell cycle, inducing oxidative stress, apoptosis and necrosis, which lead to damages of immune organs, liver, digestive tract, bone, kidney, etc., resulting in pathological changes and impaired physiological functions of these organs. Glutathione redox system, superoxide dismutase, catalase and autophagy are protective mechanisms against oxidative stress and apoptosis, and can compensate the pathological changes and physiological functions impaired by T-2 to some degree. T-2 detoxifying agents for poultry feeds include adsorbing agents (e.g., aluminosilicate-based clays and microbial cell wall), biotransforming agents (e.g., Eubacterium sp. BBSH 797 strain), and indirect detoxifying agents (e.g., plant-derived antioxidants). These T-2 detoxifying agents could alleviate different pathological changes to different degrees, and multi-component T-2 detoxifying agents can likely provide more comprehensive protection against the toxicity of T-2.
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Jing F, Zhang H, Gao M, Xue B, Cao K. RIS-Assisted Multi-Antenna AmBC Signal Detection Using Deep Reinforcement Learning. SENSORS (BASEL, SWITZERLAND) 2022; 22:6137. [PMID: 36015896 PMCID: PMC9414307 DOI: 10.3390/s22166137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Signal detection is one of the most critical and challenging issues in ambient backscatter communication (AmBC) systems. In this paper, a multi-antenna AmBC signal detection method is proposed based on reconfigurable intelligent surface (RIS) and deep reinforcement learning. Firstly, an efficient multi-antenna AmBC system is developed based on RIS, which can achieve information transmission and energy collection simultaneously. Secondly, a smart twin delayed deep deterministic (TD3) AmBC signal detection method is presented, based on deep reinforcement learning. Extensive quantitative and qualitative experiments are performed, which show that the proposed method is more compelling than the outstanding comparison methods.
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82
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Wang S, Zhao C, Xue B, Li C, Zhang X, Yang X, Li Y, Yang Y, Shen Z, Wang J, Qiu Z. Nanoalumina triggers the antibiotic persistence of Escherichia coli through quorum sensing regulators lrsF and qseB. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129198. [PMID: 35739728 DOI: 10.1016/j.jhazmat.2022.129198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Nanomaterials with bactericidal effects might provide novel strategies against bacteria. However, some bacteria can survive despite the exposure to nanomaterials, which challenges the safety of antibacterial nanomaterials. Here, we used a high dose of antibiotics to kill the E. coli. that survived under different concentrations of nanoalumina treatment to screen persisters, and found that nanoalumina could significantly trigger persisters formation. Treatment with 50 mg/L nanoalumina for 4 h resulted in the formation of (0.084 ± 0.005) % persisters. Both reactive oxygen species (ROS) and toxin-antitoxin (TA) system were involved in persisters formation. Interestingly, RT-PCR analysis and knockout of the five genes related to ROS and TA confirmed that only hipB was associated with the formation of persisters, suggesting the involvement of other mechanisms. We further identified 73 differentially expressed genes by transcriptome sequencing and analyzed them with bioinformatics tools. We selected six candidate genes and verified that five of them closely related to quorum sensing (QS) that were involved in persisters formation, and further validated that the coexpression of QS factors lrsF and qseB was a novel pathway for persisters. Our findings provided a better understanding on the emergence of bacterial persistence and the microbial behavior under nanomaterials exposure.
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Lu J, Huang J, Jin J, Xie C, Xue B, Lai J, Cheng B, Li L, Jiang Q. The Design and Characterization of a Strong Bio-Ink for Meniscus Regeneration. Int J Bioprint 2022; 8:600. [DOI: 10.18063/ijb.v8i4.600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
The meniscus is vital to the mechanical function of the knee, while it is frequently harmed because it bears a heavy load. A strong bio-ink for meniscus regeneration was prepared for the future meniscal tissue engineering. The prepared bio-ink consists of poly (vinyl alcohol) and decellularized extracellular matrix (PVA/dECM). The mechanical properties and the rheological features were explored to evaluate the effects of freezing/thawing cycles and alkaline treatment process. The printability was verified using a three-dimensional printer. The endothelial cells were employed to assess the biocompatibility. Finally, a 12-week rabbit meniscus defect model was established to evaluate the meniscus regeneration capability. We found that the bio-ink by soaking in alkaline for 40 min and 20 freezing/thawing cycles demonstrated excellent mechanical properties. The Young’s modulus reached 0.49 MPa and the stress limitation was 2.9 MPa. The results also showed good printability and biocompatibility of the proposed bio-ink in vitro. The PVA/dECM hydrogel healed the meniscus defect after 12 weeks of implantation. The articular cartilage and subchondral bone exhibited normal microstructure and composition. These results suggested that the PVA/dECM hydrogel could be a promising solution to repair meniscal lesions with preventive effects against degenerative meniscal tears and post-traumatic arthritis.
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84
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Long X, Xie J, Xue B, Li X, Sun T. Effect of oxidative modification on physicochemical and functional properties of soybean polysaccharides. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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85
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Xue B, Hui X, Chen X, Luo S, Dilrukshi H, Wu G, Chen C. Application, emerging health benefits, and dosage effects of blackcurrant food formats. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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86
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Wu J, Liu H, Wang H, Wang Y, Cheng Q, Zhao R, Gao H, Fang L, Zhu F, Xue B. iTRAQ-based quantitative proteomic analysis of the liver regeneration termination phase after partial hepatectomy in mice. J Proteomics 2022; 267:104688. [PMID: 35914716 DOI: 10.1016/j.jprot.2022.104688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/09/2022] [Accepted: 07/25/2022] [Indexed: 01/17/2023]
Abstract
Liver regeneration (LR) is an important biological process after liver injury. As the "brake" in the process of LR, the termination phase of LR not only suppresses the continuous increase in liver volume but also effectively promotes the recovery of liver function. However, the mechanisms underlying the termination phase of LR are still not clear. In our study, we used isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomic analysis to determine the protein expression profiles of livers in the termination phase of mouse LR after partial hepatectomy (PH). We found that the expression of 197 proteins increased gradually during LR; in addition, 187 proteins were upregulated and 264 proteins were downregulated specifically in the termination phase of LR. The GO analysis of the proteins revealed the upregulation of "cell-cell adhesion" and "translation" and the downregulation of the "oxidation-reduction process". The KEGG pathway analysis showed that "biosynthesis of antibiotics" and "ribosomes" were significantly upregulated, while "metabolic pathways" were significantly downregulated. These analyses indicated that the termination phase of LR mainly focuses on restoring cellular structure and function. Differentially expressed proteins such as SNX5 were also screened out from biological processes. SIGNIFICANCE: The key regulatory factors in the termination phase of LR were studied by iTRAQ-based proteomics to lay a foundation for further study of the molecular mechanism and biomarkers of the termination phase of LR. This study will guide the clinical perioperative management of patients after hepatectomy.
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87
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Xue B, Chaddha M, Elasbali AM, Zhu Z, Jairajpuri DS, Alhumaydhi FA, Mohammad T, Abdulmonem WA, Sharaf SE, Hassan MI. Death-Associated Protein Kinase 3 Inhibitors Identified by Virtual Screening for Drug Discovery in Cancer and Hypertension. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:404-413. [PMID: 35759452 DOI: 10.1089/omi.2022.0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Death-associated protein kinase 3 (DAPK3) is a serine/threonine protein kinase that regulates apoptosis, autophagy, transcription, and actin cytoskeleton reorganization. DAPK3 induces morphological alterations in apoptosis when overexpressed, and it is considered a potential drug target in antihypertensive and anticancer drug development. In this article, we report new findings from a structure-guided virtual screening for discovery of phytochemicals that could modulate the elevated expression of DAPK3, and with an eye to anticancer drug discovery. We used the Indian Medicinal Plants, Phytochemistry and Therapeutics (IMPPAT), a curated database, as part of the methodology. The potential initial hits were identified based on their physicochemical properties and binding affinity toward DAPK3. Subsequently, various filters for drug likeness followed by interaction analysis and molecular dynamics (MD) simulations for 100 nsec were performed to explore the conformational sampling and stability of DAPK3 with the candidate molecules. Notably, the data from all-atom MD simulations and principal component analysis suggested that DAPK3 forms stable complexes with ketanserin and rotenone. In conclusion, this study supports the idea that ketanserin and rotenone bind to DAPK3, and show stability, which can be further explored as promising scaffolds in drug development and therapeutics innovation in clinical contexts such as hypertension and various types of cancer.
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88
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Ding S, Sun T, Di L, Xue B. Nanostructure engineering of polymeric carbon nitride with boosted photocatalytic antibacterial activity. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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89
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Xue B, Wang D, Zhen Y, Yu R, Yang X. Reconstruction of the gradient field in the cross-section of an acoustic wave and its usefulness in processing acoustic wave fields. OPTICS EXPRESS 2022; 30:24103-24117. [PMID: 36225078 DOI: 10.1364/oe.460888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/07/2022] [Indexed: 06/16/2023]
Abstract
This paper proposes a method of reconstructing the gradient field in a cross-section of the acoustic wave using the laser beam deflection tomography, then verifing that the simultaneous acquisitions of the relative acoustic pressure distribution and the gradient field can make the direct employment of Kirchhoff's integral theorem feasible. Specifically, a position-sensitive detector (PSD) is used to sense the deflection of a laser beam impinging on a propagating acoustic wave. The deflection of the laser beam can be divided into two parts; one is in the plane that laser beams go through, and the other is perpendicular to the plane. Combining the tomographic results using the two parts of the deflection, the gradient field of the propagating acoustic wave in a cross-section is obtained, which is an extended version of beam deflection tomography. Based on the gradient of a wavefield along with the relative sound pressure distribution, Kirchhoff's integral theorem can be directly employed to calculate and analyze the wavefield further, which was hardly achieved in the past due to the lack of dense gradient sensing regimes. To verify the usefulness, two experiments are conducted, whose results indicate that the densely and precisely acquired gradient field of an acoustic wave is useful in solving the problem of port and starboard ambiguity, and the problem of accurate near-field prediction can also be well addressed, which in a deeper sense benefit from the direct employment of Kirchhoff's integral theorem in practical applications.
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90
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Xue B, DasGupta D, Alam M, Khan MS, Wang S, Shamsi A, Islam A, Hassan MI. Investigating binding mechanism of thymoquinone to human transferrin, targeting Alzheimer's disease therapy. J Cell Biochem 2022; 123:1381-1393. [PMID: 35722728 DOI: 10.1002/jcb.30299] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/20/2022] [Accepted: 06/09/2022] [Indexed: 11/09/2022]
Abstract
Iron deposition in the central nervous system (CNS) is one of the causes of neurodegenerative diseases. Human transferrin (hTf) acts as an iron carrier present in the blood plasma, preventing it from contributing to redox reactions. Plant compounds and their derivatives are frequently being used in preventing or delaying Alzheimer's disease (AD). Thymoquinone (TQ), a natural product has gained popularity because of its broad therapeutic applications. TQ is one of the significant phytoconstituent of Nigella sativa. The binding of TQ to hTf was determined by spectroscopic methods and isothermal titration calorimetry. We have observed that TQ strongly binds to hTf with a binding constant (K) of 0.22 × 106 M-1 and forming a stable complex. In addition, isothermal titration calorimetry revealed the spontaneous binding of TQ with hTf. Molecular docking analysis showed key residues of the hTf that were involved in the binding to TQ. We further performed a 250 ns molecular dynamics simulation which deciphered the dynamics and stability of the hTf-TQ complex. Structure analysis suggested that the binding of TQ doesn't cause any significant alterations in the hTf structure during the course of simulation and a stable complex is formed. Altogether, we have elucidated the mechanism of binding of TQ with hTf, which can be further implicated in the development of a novel strategy for AD therapy.
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91
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He G, Lei H, Sun W, Gu J, Yu W, Zhang D, Chen H, Li Y, Qin M, Xue B, Wang W, Cao Y. Strong and Reversible Covalent Double Network Hydrogel Based on Force-Coupled Enzymatic Reactions. Angew Chem Int Ed Engl 2022; 61:e202201765. [PMID: 35419931 DOI: 10.1002/anie.202201765] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Indexed: 12/12/2022]
Abstract
Biological load-bearing tissues are strong, tough, and recoverable under periodic mechanical loads. However, such features have rarely been achieved simultaneously in the same synthetic hydrogels. Here, we use a force-coupled enzymatic reaction to tune a strong covalent peptide linkage to a reversible bond. Based on this concept we engineered double network hydrogels that combine high mechanical strength and reversible mechanical recovery in the same hydrogels. Specifically, we found that a peptide ligase, sortase A, can promote the proteolysis of peptides under force. The peptide bond can be re-ligated by the same enzyme in the absence of force. This allows the sacrificial network in the double-network hydrogels to be ruptured and rebuilt reversibly. Our results demonstrate a general approach for precisely controlling the mechanical and dynamic properties of hydrogels at the molecular level.
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Hribar KC, Xue B, Harrod C, Jensen T, Schüler J. Abstract 1880: High throughput screening of 30 PDX cell lines in a 3D ECM hydrogel platform, incorporating tumor, stroma and immune components to demonstrate simultaneous investigation of multiple anti-tumor modalities. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
High throughput screening offers tangible benefits towards rapidly testing various permutations of novel or existing therapeutic agents. In particular, tumor panels that cover a range of histotypes and molecular subtypes have been previously developed, such as the NCI-60, however they utilize cell lines and, in some cases, a 2D cell culture format, which limit their translatability to preclinical and clinical trials. Moreover, the biological complexity of the tumor microenvironment (TME) has revealed a need for more translatable 3D in vitro tumor models that reflect the in vivo physiological outcome to therapies, particularly with the explosion of immunotherapy programs in drug discovery which target the immune compartment of the TME. Here, we describe for the first time a 3D in vitro PDX panel comprising 30 distinct PDX models in coculture with fibroblasts and PBMCs in engineered extracellular matrix hydrogels that display distinct similarities to the three compartments of the TME - tumor, stroma, and immune cells. Histotypes in the panel include, amongst others, Non-small cell lung, colorectal, breast, pancreatic, gastric, melanoma, and renal cancers. The panel is constructed in a high throughput 96-well format and rapidly assays tumor growth delay and other endpoints such as apoptosis in a dose-dependent manner across various drug modalities such as small molecules, biologics and cell therapy. The panel has been tested against targeted therapy (Docetaxel, Cisplatin) and immunomodulatory agents (Pembrolizumab, Atezolizumab) and the results correlate to the corresponding PDX in vivo data. Interestingly, cisplatin treatment displayed an average size reduction of >30% for melanoma but a varied response in NSCLC tumors. And, several NSCLC responded more favorably to checkpoint inhibitors, however, the lung epidermoid PDX demonstrated no significant response. Moreover, subsequent cytokine analysis and immunofluorescence staining of several models revealed protein signatures of cancer-associated fibroblasts and CD3+ sequestration in the tumor stroma in some 3D models, suggesting the fibroblasts’ critical role in regulating the immune response. In short, the 30-PDX Panel described here represents a large step forward towards achieving translatable efficacy data at the earliest stages of drug discovery where little is known about the mechanism of action for a particular therapeutic agent or combination of agents.
Citation Format: Kolin C. Hribar, Bin Xue, Christopher Harrod, Timothy Jensen, Julia Schüler. High throughput screening of 30 PDX cell lines in a 3D ECM hydrogel platform, incorporating tumor, stroma and immune components to demonstrate simultaneous investigation of multiple anti-tumor modalities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1880.
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Zhao C, Li J, Li C, Xue B, Wang S, Zhang X, Yang X, Shen Z, Bo L, Qiu Z, Wang J. Horizontal transfer of the multidrug resistance plasmid RP4 inhibits ammonia nitrogen removal dominated by ammonia-oxidizing bacteria. WATER RESEARCH 2022; 217:118434. [PMID: 35427829 DOI: 10.1016/j.watres.2022.118434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance genes (ARGs) have become an important public health concern. Particularly, although several ARGs have been identified in wastewater treatment plants (WWTPs), very few studies have characterized their impacts on reactor performance. Therefore, our study sought to investigate the effect of a representative conjugative transfer plasmid (RP4) encoding multidrug resistance genes on ammonia oxidation. To achieve this, we established sequencing batch reactors (SBRs) and a conjugation model with E. coli donor strains carrying the RP4 plasmid and a typical ammonia-oxidating (AOB) bacterial strain (Nitrosomonas europaea ATCC 25978) as a recipient to investigate the effect of conjugative transfer of plasmid RP4 on AOB. Our findings demonstrated that the RP4 plasmid carried by the donor strains could be transferred to AOB in the SBR and to Nitrosomonas europaea ATCC 25978. In SBR treated with donor strains carrying the RP4 plasmid, ammonia removal efficiency continuously decreased to 71%. Once the RP4 plasmid entered N. europaea ATCC 25978 in the conjugation model, ammonia removal was significantly inhibited and nitrite generation was decreased. Furthermore, the expression of several functional genes related to ammonia oxidation in AOB was suppressed following the transfer of the RP4 plasmid, including amoA, amoC, hao, nirK, and norB. In contrast, the cytL gene encoding cytochrome P460 was upregulated. These results demonstrated the ecological risk of ARGs in WWTPs, and therefore measures must be taken to avoid their transfer.
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94
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Liu B, Fan Y, Xue B, Wang T, Chao Q. Feature extraction and classification of climate change risks: a bibliometric analysis. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:495. [PMID: 35691976 PMCID: PMC9188839 DOI: 10.1007/s10661-022-10074-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Risks brought by climate change are inevitable obstacles to global development. Clarifying the features of climate change risks helps us to further understand and cope with climate change. There lacks a systematic review of climate change risks in terms of feature extraction and classification. The bibliometric analysis can be used to analyze and extract climate change risk features. The literature in the field of climate change was searched in the Web of Science database. Coauthors, citations, bibliographic coupling, co-citations, and keyword co-occurrence were analyzed. From five dimensions including nature, politics, economy, society, and culture, the risk features of climate change were extracted and summarized. Through text mining and cluster analysis, the climate change risk feature system was established, which is embodied in five different aspects: ecosystem and sustainability; uncertainty, vulnerability, and efficiency; behavior and decision-making; governance and management; and adaptation and mitigation. The feature system reflects that the current climate change risk presents strong variability and that the risk boundary is gradually blurred. The areas affected by risk are expanding and deepening. The strategies and governance for addressing risks are gradually diversified. This research contributes to the domain of climate change risk identification and assessment. The features of climate change indicate that we need to adjust policymaking and managerial practices for climate change in the future. Interdisciplinary cooperation, human cognition and preferences, public participation in global governance, and other unnatural factors related to climate change should be strengthened with a more positive attitude.
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Gong X, Zhao Z, Zhang L, Yao S, Xue B. North-south geographic heterogeneity and control strategies for polycyclic aromatic hydrocarbons (PAHs) in Chinese lake sediments illustrated by forward and backward source apportionments. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128545. [PMID: 35220116 DOI: 10.1016/j.jhazmat.2022.128545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/06/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
As universal and supervirulent pollutants, understanding the potential sources of polycyclic aromatic hydrocarbons (PAHs) in lakes is critical for formulating pollutant control policies that will ensure the ecological safety of aquatic environments. Geographic heterogeneity of PAHs in lake sediments from China nationwide was investigated to indicate north-south dissimilarities in PAH levels and sources and propose specific PAH control strategies. Geographic PAH patterns showed that higher concentrations were found in the south compared to the north due to higher energy consumption and more intense industrial activities. Furthermore, the primary contributors in the south were high molecular weight (HMW) PAHs, whereas low molecular weight (LMW) PAHs were dominant in the north. The results of forward source apportionment based on the PAH emission method (EM) were consistent with the backward method using the positive matrix factorization (PMF) model, which verified the feasibility of the combined methods. Petroleum from transport was the dominant PAH source in the south, and purifying gasoline and diesel, promoting new energy vehicles and direct injection engines might effectively reduce PAH emission. Domestic coal was the main PAH source in the north, thereby adding active substance in coal and using cleaner energy could reduce PAH release.
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Zhao C, Li C, Wang X, Cao Z, Gao C, Su S, Xue B, Wang S, Qiu Z, Wang J, Shen Z. Monitoring and evaluation of antibiotic resistance genes in three rivers in northeast China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:44148-44161. [PMID: 35122641 DOI: 10.1007/s11356-022-18555-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance genes (ARGs) have become an important public health problem. In this study, we used metagenomic sequencing to analyze the composition of ARGs in selected original habitats of northeast China, comprising three different rivers and riverbank soils of the Heilongjiang River, Tumen River, and Yalu River. Twenty types of ARG were detected in the water samples. The major ARGs were multidrug resistance genes, at approximately 0.5 copies/16S rRNA, accounting for 57.5% of the total ARG abundance. The abundance of multidrug, bacitracin, beta-lactam, macrolide-lincosamide-streptogramin, sulfonamide, fosmidomycin, and polymyxin resistance genes covered 96.9% of the total ARG abundance. No significant ecological boundary of ARG diversity was observed. The compositions of the resistance genes in the three rivers were very similar to each other, and 92.1% of ARG subtypes were shared by all water samples. Except for vancomycin resistance genes, almost all ARGs in riverbank soils were detected in the river water. About 31.05% ARGs were carried by Pseudomonas. Opportunistic pathogenic bacteria carrying resistance genes were mainly related to diarrhea and respiratory infections. Multidrug and beta-lactam resistance genes correlated positively with mobile genetic elements (MGEs), indicating a potential risk of diffusion. The composition of ARGs in three different rivers was similar, indicating that climate plays an important role in ARG occurrence. ARG subtypes in river water were almost completely the same as those in riverbank soil. ARGs had no significant geographical distribution characteristics. Many ARGs were carried by human pathogenic bacteria related to diarrhea and respiratory infections, such as Pseudomonas aeruginosa and Aeromonas caviae. In general, our results provide a valuable dataset of river water ARG distribution in northeast China. The related ecological and geographical distribution characteristics should be further explored.
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Maitiabula G, Tian F, Wang P, Zhang L, Gao X, Wan S, Sun H, Yang J, Zhang Y, Gao T, Xue B, Li C, Li J, Wang X. Liver PP2A-Cα Protects From Parenteral Nutrition-associated Hepatic Steatosis. Cell Mol Gastroenterol Hepatol 2022; 14:669-692. [PMID: 35643235 PMCID: PMC9421584 DOI: 10.1016/j.jcmgh.2022.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Parenteral nutrition (PN) is a lifesaving therapy for patients with intestinal failure. Hepatic steatosis is a potentially fatal complication of long-term PN, but the involved pathological mechanisms are incompletely unclarified. Herein, we identify the role of protein phosphatase 2A (PP2A) in the pathogenesis of parenteral nutrition-associated hepatic steatosis (PNAHS). METHODS Proteomic/phosphoproteomic analyses of liver samples from patients with PNAHS were applied to identify the mechanism of PNAHS. Total parenteral nutrition (TPN) mice model, in vivo, and in vitro experiments were used to assess the effect of PP2A-Cα on liver fatty acid metabolism. RESULTS Reduced expression of PP2A-Cα (catalytic subunit) enhanced activation of serine/threonine kinase Akt2 and decreased activation of adenosine monophosphate-activated protein kinase (AMPK) were associated with hepatic steatosis in patients with PNAHS. Mice given PN for 14 days developed hepatic steatosis, down-regulation of PP2A-Cα, activation of Akt2, and inhibition of AMPK. Hepatocyte-specific deletion of PP2A-Cα in mice given PN exacerbated Akt2 activation, AMPK inhibition, and hepatic steatosis through an effect on fatty acid degradation, whereas hepatocyte-specific PP2A-Cα overexpression significantly ameliorated hepatic steatosis accompanied with Akt2 suppression and AMPK activation. Additionally, pharmacological activation of Akt2 in mice overexpressing PP2A-Cα led to the aggravation of hepatic steatosis. CONCLUSIONS Our findings demonstrate that hepatic PP2A-Cα serves as a protective factor of PNAHS due to ameliorating hepatic steatosis and improving liver function. Our study provides a strong rationale that PP2A-Cα may be involved in the pathogenesis of PNAHS.
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Chen Y, Mou W, Guo Y, Wang J, Xue B. Experimental /numerical study of a circular rib-stiffened flange connection with inner and outer flange plates under combined bending and tensile loading. Sci Rep 2022; 12:8823. [PMID: 35614308 PMCID: PMC9133094 DOI: 10.1038/s41598-022-12896-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
Focusing on circular rib-stiffened flange connections with inner and outer flange plates, termed inner-outer flange, the mechanical behavior of the flange subjected to the combined bending and tensile loading is experimentally studied. Four nominally identical specimens were utilized to investigate the effects of the eccentricity on the mechanical behavior. The distribution of the gap between flange plates, as well as the distribution of the bolt forces, is presented. It is found that the neutral axis would gradually approach the central axis of the flange connection, as the eccentricity increases. Moreover, provided the sufficiently strong ribs, welds, and flange plates, the capacity of the flange is found to be mainly predominated by the bolt strength. A good agreement is found in the comparison of the results obtained via the finite element analysis, the semi-analytic method (SAM) and the experimental study. It corroborates the validity of using the bolt failure assumption and the plane cross-section assumption in the SAM for approximating the capacity of the inner-outer flange. In terms of the interaction of the tensile capacity with the bending capacity, the experimental results along with those in the literature are compared with the curves defined by the codes, and suggestions for design are concluded. Yield capacity, defined as the load when the bolt stress reaches the yield strength, is recommended herein for the design of a structure under in-service condition. It is found the specifications in the current codes for the rib-stiffened flanges with a single flange plate would occasionally overestimate the yield capacity of the inner-outer flanges under the combined bending and tensile loading. Moreover, both the experimental and the numerical results show a linear load interaction curve, in terms of the ultimate capacity.
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Xue B, Waseem SMA, Zhu Z, Alshahrani MA, Nazam N, Anjum F, Habib AH, Rafeeq MM, Nazam F, Sharma M. Brain-Derived Neurotrophic Factor: A Connecting Link Between Nutrition, Lifestyle, and Alzheimer’s Disease. Front Neurosci 2022; 16:925991. [PMID: 35692417 PMCID: PMC9177140 DOI: 10.3389/fnins.2022.925991] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) involving tropomyosin kinase B and low affinity p75 neurotropin receptors is the most abundant and researched neurotropins in mammal’s brain. It is one of the potential targets for therapeutics in Alzheimer’s disease (AD) owing to its key role in synaptic plasticity. Low levels of BDNF are implicated in the pathophysiology of neurological diseases including AD. However, a healthy lifestyle, exercise, and dietary modifications are shown to positively influence insulin regulation in the brain, reduce inflammation, and up-regulate the levels of BDNF, and are thus expected to have roles in AD. In this review, the relationship between BDNF, mental health, and AD is discussed. Insights into the interrelationships between nutrition, lifestyle, and environment with BDNF and possible roles in AD are also provided in the review. The review sheds light on the possible new therapeutic targets in neurodegenerative diseases.
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Zhang Y, Qin B, Zhu G, Song C, Deng J, Xue B, Gong Z, Wang X, Wu J, Shi K, Gu X, Zhang G. 论湖泊重要性及我国湖泊面临的主要生态环境问题. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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