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Ran H, Yang Y, Han W, Liang R, Zhu D, Yuan B, Xu C, Li D, Ren J, Pan H, Liu L, Ma T, Ma A, Cai L. Programmable ultrasound-mediated swarms manipulation of bacteria-red blood cell microrobots for tumor-specific thrombosis and robust photothermal therapy. Trends Biotechnol 2024:S0167-7799(24)00346-9. [PMID: 39709244 DOI: 10.1016/j.tibtech.2024.11.018] [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: 03/31/2024] [Revised: 11/12/2024] [Accepted: 11/19/2024] [Indexed: 12/23/2024]
Abstract
Despite the excellent advantages of biomicrorobots, such as autonomous navigation and targeting actuation, effective penetration and retention to deep lesion sites for effective therapy remains a longstanding challenge. Here, we present dual-engine cell microrobots, which we refer to as PR-robots, created by conjugating photosynthetic bacteria (PSB) with red blood cells (RBCs). The robots penetrate the tumor interior in swarms through combined hypoxic traction and ultrasound actuation (UA). The hypoxia-targeting ability of PSB induced PR-robot accumulation in the tumor region. Subsequently, programmable UA trapped the PR-robots to form bioswarms and traverse tissue obstacles, penetrating the tumor interior. The substantial influx of PR-robots into the tumor tissue promoted the formation of tumor-specific thrombus (TST). Finally, the PSB and TST synergistically improved the effect of photothermal therapy. Thus, these advantages of remote ultrasound control technology pave the way for various new therapies in practical biomedicine.
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Li S, Wang Y, Xie Z, Wang Y, Feng Z, Xu J, Yuan B, Zhang Y, Yang G, Wang J, Yuan Y. NLRP3 activation maintains intestinal epithelial barrier and reduces liver injury in alcoholic liver disease mice. Clin Transl Med 2024; 14:e70099. [PMID: 39605303 PMCID: PMC11602754 DOI: 10.1002/ctm2.70099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Revised: 10/27/2024] [Accepted: 11/04/2024] [Indexed: 11/29/2024] Open
Abstract
BACKGROUND Alcoholic liver disease (ALD) patients with bacterial infections usually exhibit high mortality rates. Infections frequently involve bacteria such as Vibrio vulnificus and Enterococcus faecalis. Nevertheless, the mechanisms predisposing ALD patients to bacterial infections and the role of the NLRP3 inflammasome in the intestinal epithelial barrier in ALD remain unclear. METHODS We established ALD mice models of WT, Nlrp3-/- and Gsdmd-/- through chronic alcohol consumption feeding and acute alcohol induction. We compared alterations in gut microbiota, ileitis, and adhesion protein expression, to analyze the role and potential mechanism of NLRP3 in the early onset of ALD. Concurrently, we examined the changes in inflammation and liver damage in the ileum of ALD and healthy mice following foodborne infection with V. vulnificus. RESULTS Compared with the control group, the expression levels of ZO-1, Claudin-1 and E-cadherin were reduced in the ileum of ALD mice, while those of NLRP3, caspase-1(p20), GSDMD-N and IL-1β were elevated. Nlrp3-/- and Gsdmd-/- ALD mice showed an increased gut bacterial load, decreased ileal expression of E-cadherin, more severe ileitis, pronounced liver damage, steatosis and higher plasma levels of FITC-dextran, D-LA and ZO-1 compared with WT mice. Notably, Nlrp3-/- ALD mice exhibited a higher presence of Deferribacterota and Enterobacteriaceae. Furthermore, ALD mice infected with V. vulnificus infection exhibited no further activation of NLRP3 in the ileum, leading to increased intestinal permeability and bloodstream infections. CONCLUSIONS This study indicated that NLRP3 activation in the ileum of ALD mice stabilizes the inflammation-related gut microbiota, preserves the intestinal epithelial barrier, and diminishes inflammation and liver injury. Furthermore, the compromised immune defence in ALD mice may contribute to their heightened susceptibility to bacterial pathogens. KEY POINTS Activation of the NLRP3-GSDMD pathway in the ileum of Alcoholic liver disease (ALD) mice. NLRP3 activation maintains homeostasis of gut microbiota and intestinal epithelial barrier in ALD mice. ALD mice infected with V. vulnificus infection exhibited no further activation of NLRP3 in the ileum, leading to increased intestinal permeability and bloodstream infections.
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Wu Y, Yuan Y, Yuan B, Li J, Wang J, Cui Y. Bacteriologic and Genomic Investigation of Bacillus anthracis Isolated from World War II Site, China. Emerg Infect Dis 2024; 30:2687-2689. [PMID: 39592401 PMCID: PMC11616637 DOI: 10.3201/eid3012.231520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2024] Open
Abstract
Records suggest Bacillus anthracis was used in biowarfare during World War II, but evidence remains limited. We isolated B. anthracis from soil at the remains of a World War II-era laboratory in China. Phenotypic and genomic analyses confirmed the finding, highlighting the value of microbial forensics in biothreat investigation.
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Zhu Y, Hou K, Liu J, Zhang L, Yang K, Li Y, Yuan B, Li R, Xue Y, Li H, Chang Y, Li X. Multimodel-based quantitative source apportionment and risk assessment of soil heavy metals: A reliable method to achieve regional pollution traceability and management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 956:177368. [PMID: 39500451 DOI: 10.1016/j.scitotenv.2024.177368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Revised: 10/19/2024] [Accepted: 11/01/2024] [Indexed: 11/11/2024]
Abstract
To strengthen the control of pollution sources and promote soil pollution management of agricultural land, this study constructed a comprehensive source apportionment framework, which significantly improved the reliability of potential source analysis compared with the traditional single model. The spatial distribution pattern of agricultural soil heavy metals (SHMs) content in Lintong, a typical river valley city in China, was determined and the degree of contamination was evaluated. A scientific source apportionment methodological framework was constructed through correlation analysis methods together with multiple source apportionment receptor models. Finally, the Monte Carlo simulation method was used to derive the results of the human health risk assessment (HHRA). The results revealed the following: (1) Agricultural soils were moderately and mildly polluted, accounting for 28.8 % and 71.2 % of the total number of sampling points, respectively. (2) The overall correlation of heavy metals (HMs) was strong according to the coupling analysis of the SHMs, in which a strong correlation (0.8-1) was reached among Cu, Ni, Pb, Cr and Zn, indicating that these HMs were most likely homologous or composite. (3) Multimodel analysis of the SHMs sources revealed that the first and second principal components were agricultural (41.36 %) and industrial (19.69 %) sources, respectively, and the remaining principal components were road traffic, natural factors, and atmospheric deposition or surface runoff, respectively. (4) The average comprehensive noncarcinogenic health risk indices for adults and children were 4.2259E-02 and 1.4194E-01, respectively, which were within the slight risk range, indicating that the risk caused by SHMs to the human body can be almost negligible. This study adopted a mixed method to reveal the risk of SHMs pollution and its sources, which provides some reference and technical support for traceability analysis, zoning control, and health risk studies of regional pollutants and is helpful for formulating scientific management measures and targeting control policies.
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Xu C, Ma C, Zhang W, Wei Y, Yang K, Yuan B. Membrane Fusion Mediated by Cationic Helical Peptide L-MMBen through Phosphatidylglycerol Recruitment. J Phys Chem Lett 2024; 15:11027-11034. [PMID: 39466831 DOI: 10.1021/acs.jpclett.4c02558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2024]
Abstract
Membrane fusion is the basis for many biological processes, which holds promise in biomedical applications including the creation of engineered hybrid cells and cell membrane functionalization. Extensive research efforts, including investigations into DNA zippers and carbon nanotubes, have been dedicated to the development of membrane fusion strategies inspired by natural SNARE proteins; nevertheless, achieving a delicate balance between membrane selectivity and high fusion efficiency through precise molecular engineering remains unclear. In our recent study, we successfully designed L-MMBen, a cationic helical antimicrobial peptide that exhibits remarkable antimicrobial efficacy while demonstrating moderate cytotoxicity. In this work, we demonstrate the effective and selective induction of fusion between phosphatidylglycerol (PG)-containing membranes by L-MMBen. By combining biophysical assays at the single-vesicle level with computer simulations at the molecular level, we discovered that L-MMBen can stably adsorb onto the surface of PG-containing membranes, leading to the formation of stalk structures between vesicles and ultimately resulting in membrane fusion. Furthermore, the occurrence of fusion is attributed to the unique ability of L-MMBen to recruit PG lipids and bridge adjacent vesicles. In contrast, its nonhelical counterpart DL-MMBen was found to lack this capability despite possessing an identical positive charge. These findings present an alternative molecule for achieving selective membrane fusion and provide insights for designing helical peptides with diverse applications.
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Zhang X, Liu Z, Yuan B, Yang K. Surface Wetting Behaviors of Hydroxyl-Terminated Polybutadiene: Molecular Mechanism and Modulation. Polymers (Basel) 2024; 16:3085. [PMID: 39518292 PMCID: PMC11548704 DOI: 10.3390/polym16213085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 10/26/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024] Open
Abstract
The surface wetting or coating of materials by polymers is crucial for designing functional interfaces and various industrial applications. However, the underlying mechanisms remain elusive. In this study, the wetting behavior of hydroxyl-terminated polybutadiene (HTPB) on a quartz surface was systematically investigated using computer simulation methods. A notable tip-dominant surface adsorption mode of HTPB was identified, where the hydroxyl group at the end of the polymer chain binds to the surface to initiate the wetting process. Moreover, it was found that with the increase in the degree of polymerization (e.g., from DP = 10 to 30), spontaneous adsorption of HTPB becomes increasingly difficult, with a three-fold increase in the adsorption time. These results suggest a competition mechanism between enthalpy (e.g., adhesion between the polymer and the surface) and entropy (e.g., conformational changes in polymer chains) that underlies the wetting behavior of HTPB. Based on this mechanism, two strategies were employed: altering the degree of polymerization of HTPB and/or regulating the amount of interfacial water molecules (e.g., above or below the threshold amount of 350 on a 10 × 10 nm2 surface). These strategies effectively modulate HTPB's surface wetting process. This study provides valuable insights into the mechanisms underlying the surface adsorption behavior of HTPB and offers guidance for manipulating polymer wetting processes at interfaces.
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Li Y, Hou K, Chang Y, Yuan B, Li X. A methodological study on the identification of ecological security change processes and zoning control strategies -- Based on the perspective of sustainable development. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174190. [PMID: 38936731 DOI: 10.1016/j.scitotenv.2024.174190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/03/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024]
Abstract
Ecological security (ES) is a crucial indicator for assessing the sustainable development of a region. Currently, most studies on ES primarily focus on process analysis, and the integration of environmental variability into the development of tailored control strategies for regions with varying ecological quality is overlooked. Therefore, in this study, we identified regional ES change processes, employed an optimized system to calculate the ecological security index (ESI), and identified ecological corridors (ECs) through the Minimum Constrained Resource (MCR) model to determine zoning strategies for typical arid regions, using the Ningxia region in the Yellow River Basin of China as an example. The findings showed that (1) from 2006 to 2020, the ESI values of most regions were between 0.2 and 0.4, with small but consistent increases in the ESI values over the years. (2) The proportion of regions with high ES ratings increased by 9.08 % across all districts and counties, and the center of gravity of ES shifted in a north-south and east-west direction. (3) The ESI exhibited a strong positive spatial correlation, characterized by spatial diffusion and spillover effects in most regions. (4) The ECs were predominantly distributed in a north-south direction, involving a total of 20 districts and counties. Based on the principles of sustainable development, we developed a model for the dynamic identification and zoning control of regional ES, aiming to provide a practical framework for effective ecological restoration and protection measures. Additionally, the strategies and methodologies presented in this study serve as important references for similar regions worldwide to facilitate the zoning control of ES, highlighting the broader significance and applicability of the study.
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Liang Y, Zhang Y, Huang Y, Xu C, Chen J, Zhang X, Huang B, Gan Z, Dong X, Huang S, Li C, Jia S, Zhang P, Yuan Y, Zhang H, Wang Y, Yuan B, Bao Y, Xiao S, Xiong M. Helicity-directed recognition of bacterial phospholipid via radially amphiphilic antimicrobial peptides. SCIENCE ADVANCES 2024; 10:eadn9435. [PMID: 39213359 PMCID: PMC11364095 DOI: 10.1126/sciadv.adn9435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024]
Abstract
The fundamental differences in phospholipids between bacterial and mammalian cell membranes present remarkable opportunities for antimicrobial design. However, it is challenging to distinguish bacterial anionic phospholipid phosphatidylglycerol (PG) from mammalian anionic phosphatidylserine (PS) with the same net charge. Here, we report a class of radially amphiphilic α helix antimicrobial peptides (RAPs) that can selectively discriminate PG from PS, relying on the helix structure. The representative RAP, L10-MMBen, can direct the rearrangement of PG vesicles into a lamellar structure with its helix axis parallel to the PG membrane surface. The helical structure imparts both the thermodynamic and kinetic advantages of L10-MMBen/PG assembly, and the hiding of hydrophobic regions in RAPs is crucial for PG recognition. L10-MMBen exhibits high selectivity against bacteria depending on PG recognition, showing low in vivo toxicity and significant treatment efficacy in mice infection models. Our study introduces a helicity-direct bacterial phospholipid recognition paradigm for designing highly selective antimicrobial peptides.
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Xu J, Wang J, Yuan B, Wang X, Zhang Y, Wang J, Yuan Y. Multiprobe Amplification (MPA) with Melting Curve Analysis: A Highly Stable and Cost-Effective Platform for the Simultaneous Detection of Eight Potential Bacterial Bioterrorism Agents in Complex Samples. Anal Chem 2024; 96:13679-13689. [PMID: 39110120 PMCID: PMC11339725 DOI: 10.1021/acs.analchem.4c02658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/23/2024] [Accepted: 07/30/2024] [Indexed: 08/21/2024]
Abstract
We aimed to develop an efficient detection platform that can identify a larger number of suspicious samples in a single test, saving time, manpower, and material costs, and providing vital support to the public health system in coping with the current challenging and dynamic bioterrorism threat landscape, particularly in regions of turmoil and conflict. We have successfully developed a high-throughput, multitarget fluorescent array detection platform by effectively combining integrating multiprobe amplification (MPA) with melting curve analysis. Specifically, we have established reliable laboratory testing methods for eight highly pathogenic bacteria, including Bacillus anthracis, Yersinia pestis, Brucella spp., Burkholderia pseudomallei, Francisella tularensis, Vibrio cholerae, Salmonella typhi, and Staphylococcus aureus. Our method achieves sensitive and specific simultaneous detection of eight target bacteria in one well by optimizing the reaction conditions of MPA. In the assessment of 192 simulated environmental samples, both positive and negative coincidence rates were 100.00%. Among 48 simulated clinical samples, the positive coincidence rate reached 97.73%, while maintaining a perfect negative coincidence rate of 100.00%. Moreover, the detection platform holds immense potential for attaining a more comprehensive bioterrorism screening, and its high cost-effectiveness enables the provision of diverse and adaptable diagnostic methods for public health quarantine in underdeveloped countries and regions.
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Zhang MM, Yuan B, Wang YT, Zhang FL, Liu CG, Zhao XQ. Differential Protein Expression in Set5p-Mediated Acetic Acid Stress Response and Novel Targets for Engineering Yeast Stress Tolerance. J Proteome Res 2024; 23:2986-2998. [PMID: 38396335 DOI: 10.1021/acs.jproteome.3c00617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Acetic acid is a prevalent inhibitor in lignocellulosic hydrolysate, which represses microbial growth and bioproduction. Histone modification and chromatin remodeling have been revealed to be critical for regulating eukaryotic metabolism. However, related studies in chronic acetic acid stress responses remain unclear. Our previous studies revealed that overexpression of the histone H4 methyltransferase Set5p enhanced acetic acid stress tolerance of the budding yeast Saccharomyces cerevisiae. In this study, we examined the role of Set5p in acetic acid stress by analyzing global protein expression. Significant activation of intracellular protein expression under the stress was discovered, and the functions of the differential proteins were mainly involved in chromatin modification, signal transduction, and carbohydrate metabolism. Notably, a substantial increase of Set5p expression was observed in response to acetic acid stress. Functional studies demonstrated that the restriction of the telomere capping protein Rtc3p, as well as Ies3p and Taf14p, which are related to chromatin regulation, was critical for yeast stress response. This study enriches the understanding of the epigenetic regulatory mechanisms underlying yeast stress response mediated by histone-modifying enzymes. The results also benefit the development of robust yeast strains for lignocellulosic bioconversion.
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Kuang K, Chen X, Wang M, Han W, Qiu X, Jin T, Xu R, Yuan B, Qian M, Li C, Xiang R, Li F, Zhang S, Yang Z, Du J, Li D, Zhang C, Wang Q, Jia T. Design and Discovery of New Collagen V-Derived FGF2-Blocking Natural Peptides Inhibiting Lung Squamous Cell Carcinoma In Vitro and In Vivo. J Med Chem 2024. [PMID: 39045829 DOI: 10.1021/acs.jmedchem.4c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Aberrant FGF2/FGFR signaling is implicated in lung squamous cell carcinoma (LSCC), posing treatment challenges due to the lack of targeted therapeutic options. Designing drugs that block FGF2 signaling presents a promising strategy different from traditional kinase inhibitors. We previously reported a ColVα1-derived fragment, HEPV (127AA), that inhibits FGF2-induced angiogenesis. However, its large size may limit therapeutic application. This study combines rational peptide design, molecular dynamics simulations, knowledge-based prediction, and GUV and FRET assays to identify smaller peptides with FGF2-blocking properties. We synthesized two novel peptides, HBS-P1 (45AA) and HBS-P2 (66AA), that retained the heparin-binding site. Both peptides demonstrated anti-LSCC and antiangiogenesis properties in cell viability and microvessel network induction assays. In two LSCC subcutaneous models, HBS-P1, with its affinity for FGF2 and enhanced penetration ability, demonstrated substantial therapeutic potential without apparent toxicities. Our study provides the first evidence supporting the development of collagen V-derived natural peptides as FGF2-blocking agents for LSCC treatment.
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Liu K, Yuan B, Zhang J. An Exact Theory of Causal Emergence for Linear Stochastic Iteration Systems. ENTROPY (BASEL, SWITZERLAND) 2024; 26:618. [PMID: 39202088 PMCID: PMC11354030 DOI: 10.3390/e26080618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/09/2024] [Accepted: 07/20/2024] [Indexed: 09/03/2024]
Abstract
After coarse-graining a complex system, the dynamics of its macro-state may exhibit more pronounced causal effects than those of its micro-state. This phenomenon, known as causal emergence, is quantified by the indicator of effective information. However, two challenges confront this theory: the absence of well-developed frameworks in continuous stochastic dynamical systems and the reliance on coarse-graining methodologies. In this study, we introduce an exact theoretic framework for causal emergence within linear stochastic iteration systems featuring continuous state spaces and Gaussian noise. Building upon this foundation, we derive an analytical expression for effective information across general dynamics and identify optimal linear coarse-graining strategies that maximize the degree of causal emergence when the dimension averaged uncertainty eliminated by coarse-graining has an upper bound. Our investigation reveals that the maximal causal emergence and the optimal coarse-graining methods are primarily determined by the principal eigenvalues and eigenvectors of the dynamic system's parameter matrix, with the latter not being unique. To validate our propositions, we apply our analytical models to three simplified physical systems, comparing the outcomes with numerical simulations, and consistently achieve congruent results.
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Zhang JL, Yuan B, Zhang XW, Zhang H, Wang H, Wang XZ, Zhao HW. X-ray Opaque Polymer Drug-Eluting Beads Loaded with Iodized Oil: Preparation and In Vitro and In Vivo Evaluations. ACS OMEGA 2024; 9:31353-31358. [PMID: 39072120 PMCID: PMC11270547 DOI: 10.1021/acsomega.3c09368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/19/2024] [Accepted: 07/04/2024] [Indexed: 07/30/2024]
Abstract
Drug-eluting microspheres are commonly used as a local drug delivery system for interventional therapy. However, current drug-eluting microspheres have poor X-ray visibility, which can hinder tracking and postembolization evaluation. In the current study, X-ray-visible poly(acrylic acid) drug-eluting beads loaded with iodized oil (IO-PAA-DEBs) ranging from 100-300 μm were prepared and evaluated both in vitro and in vivo. Iodized oil served as the radiopaque agent, and X-ray and computed tomography scanning confirmed that the microspheres exhibited excellent X-ray-visible properties. The drug-loading capacities of bleomycin hydrochloride, doxorubicin hydrochloride, and oxaliplatin were also investigated. IO-PAA-DEBs exhibited sustained drug release properties, accompanied by a cumulative drug release rate that reached approximately 60% after 120 h. In vitro and in vivo experiments revealed that IO-PAA-DEBs had good biocompatibility. Collectively, these results demonstrated that IO-PAA-DEBs could facilitate transarterial embolization and sustained drug delivery.
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Wei L, Tu W, Xu Y, Xu C, Dou Y, Ge Y, Sun S, Wei Y, Yang K, Yuan B. Assembly-Induced Membrane Selectivity of Artificial Model Peptides through Entropy-Enthalpy Competition. ACS NANO 2024; 18:18650-18662. [PMID: 38959157 DOI: 10.1021/acsnano.4c05265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Peptide design and drug development offer a promising solution for combating serious diseases or infections. In this study, using an AI-human negotiation approach, we have designed a class of minimal model peptides against tuberculosis (TB), among which K7W6 exhibits potent efficacy attributed to its assembly-induced function. Comprising lysine and tryptophan with an amphiphilic α-helical structure, the K7W6 sequence exhibits robust activity against various infectious bacteria causing TB (including clinically isolated and drug-resistant strains) both in vitro and in vivo. Moreover, it synergistically enhances the effectiveness of the first-line antibiotic rifampicin while displaying low potential for inducing drug resistance and minimal toxicity toward mammalian cells. Biophysical experiments and simulations elucidate that K7W6's exceptional performance can be ascribed to its highly selective and efficient membrane permeabilization activity induced by its distinctive self-assembly behavior. Additionally, these assemblies regulate the interplay between enthalpy and entropy during K7W6-membrane interaction, leading to the peptide's two-step mechanism of membrane interaction. These findings provide valuable insights into rational design principles for developing advanced peptide-based drugs while uncovering the functional role played by assembly.
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Zhou Y, Zhang X, Yuan B, Lu D, Zhuang GL, Du P. Enantiomerically Resolvable Inherent Chirality Induced by Strong Para-Steric Hindrance in Cycloparaphenylene-Based Carbon Nanohoops. Org Lett 2024; 26:5635-5639. [PMID: 38958212 DOI: 10.1021/acs.orglett.4c01509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The chemical modification of the achiral carbon nanohoops to break the symmetry will result in inherently chiral structures with interesting optical properties. Herein, we report two novel π-extended chiral macrocycles, cyclo[10]paraphenylene-pyrene ([10]CPP-2Pyrene) and cyclo[10]paraphenylene-hexa-peri-hexabenzocoronene ([10]CPP-2HBC). The large substituents on the nanohoop peripheries effectively prevented free rotation and the racemization process. The conformation of each enantiomer is stable enough to be resolved by recycling HPLC.
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Li L, Li D, Geng Z, Huo Z, Kang Y, Guo X, Yuan B, Xu B, Wang T. Causal relationship between bone mineral density and intervertebral disc degeneration: a univariate and multivariable mendelian randomization study. BMC Musculoskelet Disord 2024; 25:517. [PMID: 38970068 PMCID: PMC11225368 DOI: 10.1186/s12891-024-07631-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND Although previous studies have suggested a possible association between bone mineral density (BMD) and intervertebral disc degeneration (IDD), the causal relationship between them remains unclear. Evidence from accumulating studies indicates that they might mutually influence one another. However, observational studies may be affected by potential confounders. Meanwhile, Mendelian randomization (MR) study can overcome these confounders to assess causality. OBJECTIVES This Mendelian randomization (MR) study aimed to explore the causal effect of bone mineral density (BMD) on intervertebral disc degeneration (IDD). METHODS Summary data from genome-wide association studies of bone mineral density (BMD) and IDD (the FinnGen biobank) have been acquired. The inverse variance weighted (IVW) method was utilized as the primary MR analysis approach. Weighted median, MR-Egger regression, weighted mode, and simple mode were used as supplements. The Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) and MR-Egger regression were performed to assess horizontal pleiotropy. Cochran's Q test evaluated heterogeneity. Leave-one-out sensitivity analysis was further conducted to determine the reliability of the causal relationship. Multivariate MR (MVMR) analyses used multivariable inverse variance-weighted methods to individually and jointly adjust for four potential confounders, body mass index (BMI), Type2 diabetes, hyperthyroidism and smoking. A reverse MR analysis was conducted to assess potential reverse causation. RESULTS In the univariate MR analysis, femoral neck bone mineral density (FNBMD), heel bone mineral density (eBMD), lumbar spine bone mineral density (LSBMD), and total body bone mineral density (TB BMD) had a direct causal effect on intervertebral disc degeneration (IDD) [FNBMD-related analysis: OR(95%CI) = 1.17 (1.04 to 1.31), p = 0.008, eBMD-related analysis: OR(95%CI) = 1.06 (1.01 to 1.12), p = 0.028, LSBMD-related analysis: OR(95%CI) = 1.20 (1.10 to 1.31), p = 3.38E-7,TB BMD-related analysis: OR(95%CI) = 1.20 (1.12 to 1.29), p = 1.0E-8]. In the MVMR analysis, it was revealed that, even after controlling for confounding factors, heel bone mineral density (eBMD), lumbar spine bone mineral density (LSBMD), and total body bone mineral density (TB BMD) still maintained an independent and significant causal association with IDD(Adjusting for heel bone mineral density: beta = 0.073, OR95% CI = 1.08(1.02 to 1.14), P = 0.013; Adjusting for lumbar spine bone mineral density: beta = 0.11, OR(95%CI) = 1.12(1.02 to 1.23), P = 0.03; Adjusting for total body bone mineral density: beta = 0.139, OR95% CI = 1.15(1.06 to 1.24), P = 5.53E - 5). In the reverse analysis, no evidence was found to suggest that IDD has an impact on BMD. CONCLUSIONS The findings from our univariate and multivariable Mendelian randomization analysis establish a substantial positive causal association between BMD and IDD, indicating that higher bone mineral density may be a significant risk factor for intervertebral disc degeneration. Notably, no causal effect of IDD on these four measures of bone mineral density was observed. Further research is required to elucidate the underlying mechanisms governing this causal relationship.
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Yuan B, Qi Y, Zhang X, Hu J, Fan Y, Ji X. The relationship of MITF gene expression and promoter methylation with plumage colour in quail. Br Poult Sci 2024; 65:259-264. [PMID: 38578288 DOI: 10.1080/00071668.2024.2326962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/16/2024] [Indexed: 04/06/2024]
Abstract
1. This study focused on the relationship between MITF mRNA expression and plumage colour in quail and the effect of promoter methylation on the expression of MITF mRNA.2. The CDS region of MITF mRNA was cloned by RT-PCR, followed by DNA sequencing. The RT-qPCR method was used to analyse the expression levels of MITF mRNA in dorsal skin tissue in Korean quail and Beijing white quail. The promoter region of the MITF gene was cloned, and the CpG island was predicted by the CpGplot program. The methylation levels of the CpG island were analysed using BS-PCR technology.3. Quail MITF mRNA contains a 1,476 bp complete ORF, which encodes a 492 amino acid residue protein. The MITF protein has no signal peptide or transmembrane region. The expression of MITF mRNA in dorsal tissue of Korean quail was significantly higher than that in Beijing white quail (p < 0.01). Abundant cis-elements and a 346 bp CpG island were found in the promoter region of the MITF gene. The average methylation level of the CpG island was 22 (22%) in Korean quail, and 46 (30%) in Beijing white quail (p < 0.05).4. The hypermethylation of the MITF gene promoter region in Beijing white quail resulted in a decrease in expression level, which was related to white feather colour.
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Wang X, Wang Q, Li G, Xu H, Liu B, Yuan B, Zhou Y, Li Y. Identifying the protective effects of miR-874-3p/ATF3 axis in intervertebral disc degeneration by single-cell RNA sequencing and validation. J Cell Mol Med 2024; 28:e18492. [PMID: 38890795 PMCID: PMC11187931 DOI: 10.1111/jcmm.18492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/14/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Intervertebral disc degeneration (IVDD) severely affects the work and the quality of life of people. We previously demonstrated that silencing activation transcription factor 3 (ATF3) blocked the IVDD pathological process by regulating nucleus pulposus cell (NPC) ferroptosis, apoptosis, inflammation, and extracellular matrix (ECM) metabolism. Nevertheless, whether miR-874-3p mediated the IVDD pathological process by targeting ATF3 remains unclear. We performed single-cell RNA sequencing (scRNA-seq) and bioinformatics analysis to identify ATF3 as a key ferroptosis gene in IVDD. Then, Western blotting, flow cytometry, ELISA, and animal experiments were performed to validate the roles and regulatory mechanisms of miR-874-3p/ATF3 signalling axis in IVDD. ATF3 was highly expressed in IVDD patients and multiple cell types of IVDD rat, as revealed by scRNA-seq and bioinformatics analysis. GO analysis unveiled the involvement of ATF3 in regulating cell apoptosis and ECM metabolism. Furthermore, we verified that miR-874-3p might protect against IVDD by inhibiting NPC ferroptosis, apoptosis, ECM degradation, and inflammatory response by targeting ATF3. In vivo experiments displayed the protective effect of miR-874-3p/ATF3 axis on IVDD. These findings propose the potential of miR-874-3p and ATF3 as biomarkers of IVDD and suggest that targeting the miR-874-3p/ATF3 axis may be a therapeutic target for IVDD.
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Guo Z, Yue N, Chen M, Li J, Lv R, Wang J, Liu T, Huang J, Gao S, Li Y, Yuan B, Wang J, Kang L, Ji B, Xin W. Purinergic Receptor Antagonists Inhibit Hemolysis Induced by Clostridium perfringens Alpha Toxin. Pathogens 2024; 13:454. [PMID: 38921752 PMCID: PMC11206506 DOI: 10.3390/pathogens13060454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/28/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024] Open
Abstract
Clostridium perfringens alpha toxin (CPA), which causes yellow lamb disease in sheep and gas gangrene and food poisoning in humans, is produced by all types of C. perfringens and is the major virulence determinant of C. perfringens type A. CPA induces hemolysis in many species, including humans, murines, sheep and rabbits, through its enzymatic activity, which dissolves the cell membrane. Recent studies have shown that some pore-forming toxins cause hemolysis, which is achieved by the activation of purinergic receptors (P2). However, the relationship between P2 receptors and non-pore-forming toxin hemolysis has not been investigated. In the present study, we examined the function of P2 receptors in CPA toxin hemolysis and found that CPA-induced hemolysis was dependent on P2 receptor activation, and this was also true for Staphylococcus aureus β-Hemolysin, another non-pore-forming toxin. Furthermore, we use selective P2 receptor antagonists to demonstrate that P2X1 and P2X7 play important roles in the hemolysis of human and murine erythrocytes. In addition, we found that redox metabolism was mainly involved in CPA-induced hemolysis using metabolomic analysis. We further demonstrate that CPA activates P2 receptors and then activates NADPH oxidase through the PI3K/Akt and MEK1/ERK1 pathways, followed by the production of active oxygen to induce hemolysis. These findings contribute to our understanding of the pathological effects of CPA, clarify the relationship between P2 activation and non-pore-forming toxin-induced hemolysis, and provide new insights into CPA-induced hemolysis.
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Kong X, Zhang X, Yuan B, Zhang W, Lu D, Du P. Synthesis and Photophysical Properties of a Chiral Carbon Nanoring Containing Rubicene. J Org Chem 2024. [PMID: 38771292 DOI: 10.1021/acs.joc.4c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Herein we report the construction of an inherently chiral carbon nanoring, cyclo[7]paraphenylene-2,9-rubicene ([7]CPPRu2,9), by combining rubicene with a C-shaped synthon through the Suzuki-Miyaura coupling reaction. The structure was fully confirmed by high-resolution mass spectroscopies (HR-MS) and various NMR techniques. The photophysical properties were investigated by UV-vis absorption and fluorescence spectroscopy as well as the time-resolved fluorescence decay. Moreover, two enantiomers (M)/(P)-[7]CPPRu2,9 were successfully resolved by recyclable HPLC and studied by CD and CPL spectra.
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Yuan B, Hou K, Li Y, Sun P. A coupling model based on spatial characteristics and evolution of terrestrial ecosystem carbon storage: a case study of Hanzhong. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:32725-32745. [PMID: 38662295 DOI: 10.1007/s11356-024-33441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Ecosystem carbon storage (ECS) is a critical consideration in reducing the impact of global warming and tackling environmental challenges, positioning it at the forefront of contemporary research. Due to the significant differences in the influence of land usage patterns on ECS in various policy contexts and China's commitment to attaining a carbon-neutral status, a model simulating different scenarios is needed to analyze the spatiotemporal characteristics and evolutionary process of carbon storage in terrestrial ecosystems accurately. To address this challenge, this study established a coupling model of "Geographical analysis -Evolution analysis -Predicting (GEP)" for assessing ecosystem ECS and analyzing its spatial characteristics and evolutionary patterns and projecting the spatial distribution of ECS under various developmental scenarios, which analyzed variations in ECS across different levels of magnitude and delineated the changing areas across a range of varying scenarios in the future additionally. The outcomes suggested that the ECS decreased by 1.17 × 106 t from 1990 to 2020, which pertaining to the utilization transfer of land in the area, whose change in ECS levels with a positive trend. It is predicted that the ECS will grow by 1.15 × 106 t and 1.44 × 106 t, in 2030 and 2060 compared with 2020 within the framework of natural development scenario (NDS), while within the framework of ecological protection scene (EPS), ECS will increase significantly, increasing by 3.06 × 106 t and 4.44 × 106 t. There will be more areas where ECS increases within the framework of EPS, by comparing with the NDS. This study offers a comprehensive analysis of Hanzhong City's carbon storage trends, demonstrating its significant impact on climate change mitigation and serving as a predictive model for similar regions, which underscores the importance of localized carbon management strategies, offering valuable insights for local governments in formulating effective climate adaptation and mitigation policies.
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Zhang JL, Yuan B, Zhang H, Wang MQ. Transcatheter arterial embolization with N-butyl cyanoacrylate for postoperative hemorrhage treatment following pancreatoduodenectomy. Emerg Radiol 2024; 31:179-185. [PMID: 38334821 DOI: 10.1007/s10140-024-02211-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
PURPOSE Postoperative hemorrhage (PPH) is a severe complication of pancreatoduodenectomy (PD) with a mortality rate of 5-20.2% and mortality due to hemorrhage of 11-58%. Transcatheter arterial embolization (TAE) has been widely recommended for PPH, however, TAE with N-butyl cyanoacrylate (NBCA) for PPH treatment has been reported rarely. Therefore, this study aimed to evaluate the safety and efficacy of TAE with NBCA for PPH treatment following PD. METHODS This retrospective study included 14 male patients (mean age, 60.93 ± 10.97 years) with postoperative hemorrhage following PD treated with TAE using NBCA as the main embolic agent from October 2019 to February 2022. The clinical data, technical and success rate, and complications were analyzed. RESULTS Among the 14 patients who underwent TAE, the technical and clinical success rates were 100 and 85.71%, respectively. Angiography revealed contrast extravasation in 12 cases and a pseudoaneurysm in 3 cases. One patient developed a serious infection and died 2 days after the TAE. CONCLUSION TAE with NBCA for PPH treatment following PD, especially for massive hemorrhage caused by a pancreatic fistula, biliary fistula, or inflammatory corrosion, can result in rapid and effective hemostasis with high safety.
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Yuan B, Wang WB, Wang YT, Zhao XQ. Regulatory mechanisms underlying yeast chemical stress response and development of robust strains for bioproduction. Curr Opin Biotechnol 2024; 86:103072. [PMID: 38330874 DOI: 10.1016/j.copbio.2024.103072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/10/2024]
Abstract
Yeast is widely studied in producing biofuels and biochemicals using renewable biomass. Among various yeasts, Saccharomyces cerevisiae has been particularly recognized as an important yeast cell factory. However, economic bioproduction using S. cerevisiae is challenged by harsh environments during fermentation, among which inhibitory chemicals in the culture media or toxic products are common experiences. Understanding the stress-responsive mechanisms is conducive to developing robust yeast strains. Here, we review recent progress in mechanisms underlying yeast stress response, including regulation of cell wall integrity, membrane transport, antioxidative system, and gene transcription. We highlight epigenetic regulation of stress response and summarize manipulation of yeast stress tolerance for improved bioproduction. Prospects in the application of machine learning to improve production efficiency are also discussed.
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Zhang Z, Ou L, Yang K, Yuan B. Energy and Speed Landscapes of the Membrane Internalization Behavior of Soft Nanoparticles. J Phys Chem B 2024; 128:2632-2639. [PMID: 38467492 DOI: 10.1021/acs.jpcb.3c07177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The cellular endocytosis of nanoparticles (NPs) is a fundamental biological process with significant potential in biomedical applications. However, a comprehensive understanding of the mechanistic aspects of endocytosis and the impact of particle properties on this process remains elusive. In this study, we investigated the membrane-wrapping behavior of soft NPs (SNPs) with varying rigidities using theoretical calculations. Our findings reveal that the membrane-wrapping process of SNPs involves a complex energy change including the possible existence of an energy barrier; moreover, it is found that the location and height of this barrier strongly depend on the mechanistic properties of the NPs and membranes. Additionally, by considering force balance in the membrane-wrapping process, we calculated the speed at which NP is internalized by the membrane, showing a nonmonotonic dependence on particle rigidity and/or wrapping degree. These phenomena can be attributed to competition between different energy components associated with NP-membrane binding, membrane tension, and deformations occurring during SNP-membrane interaction processes. Our results contribute to a deeper understanding of cellular-level endocytosis mechanisms and offer potential applications for soft NPs in biomedicine.
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Zhang JL, Zhang XW, Yuan B, Zhang H, Wang XZ, Wang H, Zhao HW. Supramolecular Chemotherapy: Complexation by Carboxylated Pillar[6]arene for Decreasing Cytotoxicity of Nitrogen Mustard to Normal Cells and Enhancing Its Antitumor Efficiency against Breast Cancer. ACS OMEGA 2024; 9:11829-11835. [PMID: 38497008 PMCID: PMC10938388 DOI: 10.1021/acsomega.3c09353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Advances in chemotherapeutic strategies are urgently required to improve antitumor efficiency. Herein, a carboxylated pillar[6]arene (CP6A) was employed to load chemotherapy medication, nitrogen mustard (NM), via forming a direct host-guest complex, as this helps to decrease the cytotoxicity of NM on normal mammary epithelial cells. Attributed to the stronger complexation ability of CP6A for endogenous spermine (SPM) than for NM, the complexed NM could be competitively released from the CP6A cavity via replacement with SPM. This chemotherapy strategy performed well in vitro and in vivo for SPM-overexpressed cancers. In comparison with free NM, antitumor efficiency of NM/CP6A was significantly enhanced, which originated from the synergistic effect of competitive release of NM and simultaneous trapping of SPM. This strategy might guide expansion to other first-line antitumor agents to improve therapeutic efficacy and decrease side effects, thereby replenishing the possibilities of supramolecular chemotherapy.
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