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Chen Y, Wang J, Zheng C, Liu Z. Cryo-Electron Microscopy in the Study of Antiviral Innate Immunity. Methods Mol Biol 2025; 2854:177-188. [PMID: 39192129 DOI: 10.1007/978-1-0716-4108-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 08/29/2024]
Abstract
Cryo-electron microscopy is a powerful methodology in structural biology and has been broadly used in high-resolution structure determination for challenging samples, which are not readily available for traditional techniques. In particular, the strength of super macro-complexes and the lack of a need for crystals for cryo-EM make this technique feasible for the structural study of complexes involved in antiviral innate immunity. This chapter presents detailed information and experimental procedures of Cryo-EM for determining the structures of the complexes using STING as an example. The procedures included a sample quality check, high-resolution data acquisition, and image processing for Cryo-EM 3D structure determination.
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Affiliation(s)
- Yan Chen
- School of Medicine, Shaoguan University, Shaoguan, Guangdong, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, the Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Jingyu Wang
- Distinct HealthCare Medical Center, Changsha Section, Shenzhen, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, the Chinese University of Hong Kong, Shenzhen, Guangdong, China.
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2
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Zhang QL, Wang YJ, Song WG, Sun MG, Liu SM, Yang RY. Electrostatic-Field-Induced Collapse of Nanobubbles in Nanochannels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 39141493 DOI: 10.1021/acs.langmuir.4c01647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 08/16/2024]
Abstract
The adsorbed nanobubbles inside the nanochannels can cause fluid transport blockages, which will obviously degrade the nanodevice performance and reduce the lifetime. However, due to small-scale effects, the removal of nanobubbles is a huge challenge at the nanoscale. Herein, molecular dynamics simulations are carried out to study the effect of the electrostatic field on underwater nitrogen nanobubbles confined in nanochannels. It is found that the nanobubbles will collapse under an appropriate electrostatic field, thereby unblocking the transport of water in the nanochannels. The formation of ordered water structures induced by electrostatic fields plays an important role in the removal of nanobubbles from the nanochannels. Our findings provide a convenient, controllable, and remote way to address the blockage problem of nanobubbles in nanochannels, which may have potential applications in improving the performance of fuel cells.
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Affiliation(s)
- Qi-Lin Zhang
- School of Mathematics-Physics and Finance and School of Materials Science and Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, People's Republic of China
| | - Yun-Jie Wang
- School of Mathematics-Physics and Finance and School of Materials Science and Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, People's Republic of China
| | - Wen-Guang Song
- National University of Defense Technology, Nanjing, Jiangsu 210039, People's Republic of China
| | - Ming-Guo Sun
- School of Mathematics-Physics and Finance and School of Materials Science and Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, People's Republic of China
| | - Shao-Min Liu
- School of Mathematics-Physics and Finance and School of Materials Science and Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, People's Republic of China
| | - Rong-Yao Yang
- Hunan Provincial Key Laboratory of Intelligent Sensors and Advanced Sensor Materials, School of Physics and Electronics, Hunan University of Science and Technology, Xiangtan, Hunan 411201, People's Republic of China
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3
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Liu W, Zheng F, Ma C, Xu W, Chen Y, Sha J. Single-Digit Nanobubble Sensing via Nanopore Technology. Anal Chem 2024; 96:9544-9550. [PMID: 38809167 DOI: 10.1021/acs.analchem.4c01035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 05/30/2024]
Abstract
Nanobubbles play an important role in diverse fields, including engineering, medicine, and agriculture. Understanding the characteristics of individual nanobubbles is essential for comprehending fluid dynamics behaviors and advancing nanoscale science across various fields. Here, we report a strategy based on nanopore sensors for characterizing single-digit nanobubbles. We investigated the sizes and diffusion coefficients of nanobubbles at different voltages. Additionally, the finite element simulation and molecular dynamics simulation were introduced to account for counterion concentration variation around nanobubbles in the nanopore. In particular, the differences in stability and surface charge density of nanobubbles under various solution environments have been studied by the ion-stabilized model and the DLVO theory. Additionally, a straightforward method to mitigate nanobubble generation in the bulk for reducing current noise in nanopore sensing was suggested. The results hold significant implications for enhancing the understanding of individual nanobubble characterizations, especially in the nanofluid field.
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Affiliation(s)
- Wei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Department of Chemistry & Chemical Engineering, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Fei Zheng
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
- School of Nanoscience and Nanotechnology, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chaofan Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Wei Xu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
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Choudhary A, Ho TA. Confinement-induced clustering of H 2 and CO 2 gas molecules in hydrated nanopores. Phys Chem Chem Phys 2024; 26:10506-10514. [PMID: 38380805 DOI: 10.1039/d3cp06024a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 02/22/2024]
Abstract
Gas molecule clustering within nanopores holds significance in the fields of nanofluidics, biology, gas adsorption/desorption, and geological gas storage. However, the intricate roles of nanoconfinement and surface chemistry that govern the formation of gas clusters remain inadequately explored. In this study, through free energy calculation in molecular simulations, we systematically compared the tendencies of H2 and CO2 molecules to aggregate within hydrated hydrophobic pyrophyllite and hydrophilic gibbsite nanopores. The results indicate that nanoconfinement enhances gas dimer formation in the nanopores, irrespective of surface chemistry. However, surface hydrophilicity prohibits the formation of gas clusters larger than dimers, while large gas clusters form easily in hydrophobic nanopores. Despite H2 and CO2 both being non-polar, the larger quadrupole moment of CO2 leads to a stronger preference for dimer/cluster formation compared to H2. Our results also indicate that gases prefer to enter the nanopores as individual molecules, but exit the nanopores as dimers/clusters. This investigation provides a mechanistic understanding of gas cluster formation within nanopores, which is relevant to various applications, including geological gas storage.
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Affiliation(s)
- Aditya Choudhary
- Geochemistry Department, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Tuan A Ho
- Geochemistry Department, Sandia National Laboratories, Albuquerque, NM 87185, USA.
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Rabinowitz J, Hartel AJW, Dayton H, Fabbri JD, Jo J, Dietrich LEP, Shepard KL. Charge Mapping of Pseudomonas aeruginosa Using a Hopping Mode Scanning Ion Conductance Microscopy Technique. Anal Chem 2023; 95:5285-5292. [PMID: 36920847 PMCID: PMC10359948 DOI: 10.1021/acs.analchem.2c05303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 03/16/2023]
Abstract
Scanning ion conductance microscopy (SICM) is a topographic imaging technique capable of probing biological samples in electrolyte conditions. SICM enhancements have enabled surface charge detection based on voltage-dependent signals. Here, we show how the hopping mode SICM method (HP-SICM) can be used for rapid and minimally invasive surface charge mapping. We validate our method usingPseudomonas aeruginosaPA14 (PA) cells and observe a surface charge density of σPA = -2.0 ± 0.45 mC/m2 that is homogeneous within the ∼80 nm lateral scan resolution. This biological surface charge is detected from at least 1.7 μm above the membrane (395× the Debye length), and the long-range charge detection is attributed to electroosmotic amplification. We show that imaging with a nanobubble-plugged probe reduces perturbation of the underlying sample. We extend the technique to PA biofilms and observe a charge density exceeding -20 mC/m2. We use a solid-state calibration to quantify surface charge density and show that HP-SICM cannot be quantitatively described by a steady-state finite element model. This work contributes to the body of scanning probe methods that can uniquely contribute to microbiology and cellular biology.
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Affiliation(s)
- Jake Rabinowitz
- Department of Electrical Engineering, Columbia University, New York, New York 10027, United States
| | - Andreas J W Hartel
- Department of Electrical Engineering, Columbia University, New York, New York 10027, United States.,Department of Biology, Columbia University, New York, New York 10027, United States
| | - Hannah Dayton
- Department of Biology, Columbia University, New York, New York 10027, United States
| | - Jason D Fabbri
- Department of Electrical Engineering, Columbia University, New York, New York 10027, United States
| | - Jeanyoung Jo
- Department of Biology, Columbia University, New York, New York 10027, United States
| | - Lars E P Dietrich
- Department of Biology, Columbia University, New York, New York 10027, United States
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, New York 10027, United States
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Zhang L, Liu F, Wang J, Lin H, Han Q. Bioinspired nanobubble water channel membranes for ultrafast osmosis desalination. J Memb Sci 2023. [DOI: 10.1016/j.memsci.2023.121554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 03/08/2023]
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7
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Nanobubble-governed membrane with nanofluidic channels for efficient molecule/ion sieving. J Memb Sci 2023. [DOI: 10.1016/j.memsci.2023.121402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/30/2023]
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Abstract
This paper reviews recent developments in the fundamental understating of ultrafine (nano) bubbles (NBs) and presents technological advances and reagent types used for their generation in flotation. The generation of NBs using various approaches including ultrasonication, solvent exchange, temperature change, hydrodynamic cavitation, and electrolysis was assessed. Most importantly, restrictions and opportunities with respect to the detection of NBs were comprehensively reviewed, focusing on various characterization techniques such as the laser particle size analyzer (LPSA), nanoparticle tracking (NTA), dynamic light scattering (DLS), zeta-phase light scattering (ZPALS), and zeta sizer. As a key feature, types and possible mechanisms of surfactants applied to stabilize NBs were also explored. Furthermore, flotation-assisted nano-bubbles was reported as an efficient method for recovering minerals, with a special focus on flotation kinetics. It was found that most researchers reported the existence and formation of NBs by different techniques, but there is not enough information on an accurate measurement of their size distribution and their commonly used reagents. It was also recognized that a suitable method for generating NBs, at a high rate and with a low cost, remains a technical challenge in flotation. The application of hydrodynamic cavitation based on a venturi tube and using the LPSA and NTA in laboratory scales were identified as the most predominant approaches for the generation and detection of NBs, respectively. In this regard, neither pilot- nor industrial-scale case studies were found in the literature; they were only highlighted as future works. Although the NB-stabilizing effects of electrolytes have been well-explored, the mechanisms related to surfactants remain the issue of further investigation. The effectiveness of the NB-assisted flotation processes has been mostly addressed for single minerals, and only a few works have been reported for bulk materials. Finally, we believe that the current review paves the way for an appropriate selection of generating and detecting ultrafine bubbles and shines the light on a profound understanding of its effectiveness.
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Zhou Y, Sun L, Watanabe S, Ando T. Recent Advances in the Glass Pipet: from Fundament to Applications. Anal Chem 2021; 94:324-335. [PMID: 34841859 DOI: 10.1021/acs.analchem.1c04462] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yuanshu Zhou
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Linhao Sun
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Shinji Watanabe
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Toshio Ando
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
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Liu Z, Cao Z, He J, Zhang H, Ge Y, Chen B. Versatile Printing of Substantial Liquid Cells for Efficiently Imaging In Situ Liquid-Phase Dynamics. NANO LETTERS 2021; 21:6882-6890. [PMID: 34387492 DOI: 10.1021/acs.nanolett.1c01901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 06/13/2023]
Abstract
Through its ability to image liquid-phase dynamics at nano/atomic-scale resolution, liquid-cell electron microscopy is essential for a wide range of applications, including wet-chemical synthesis, catalysis, and nanoparticle tracking, for which involved structural features are critical. However, statistical investigations by usual techniques remain challenging because of the difficulty in fabricating substantial liquid cells with appreciable efficiency. Here, we report a general approach for efficiently printing huge numbers of ready-to-use liquid cells (∼9000) within 30 s by electrospinning, with the unique feature of statistical liquid-phase studies requiring only one experimental time slot. Our solution efficiently resolves a complete transition picture of bubble evolution and also the induced nanoparticle motion. We statistically quantify the effect of the electron dose rate on the bubble variation and conclude that the bubble-driven nanoparticle motion is a ballistic-like behavior insignificant to morphological asymmetries. The versatile approach here is critical for statistical research, offering great opportunities in liquid-phase-associated dynamic studies.
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Affiliation(s)
- Zhiwen Liu
- Center for Ultrafast Science and Technology, School of Physics and Astronomy, and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Zetan Cao
- Center for Ultrafast Science and Technology, School of Physics and Astronomy, and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Jia He
- Center for Ultrafast Science and Technology, School of Physics and Astronomy, and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Haoran Zhang
- Center for Ultrafast Science and Technology, School of Physics and Astronomy, and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Yujun Ge
- Center for Ultrafast Science and Technology, School of Physics and Astronomy, and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Bin Chen
- Center for Ultrafast Science and Technology, School of Physics and Astronomy, and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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Zhou L, Wang S, Zhang L, Hu J. Generation and stability of bulk nanobubbles: A review and perspective. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2021.101439] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/20/2022]
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