1
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Son R, Yamazawa K, Oguchi A, Suga M, Tamura M, Yanagita M, Murakawa Y, Kume S. Morphomics via next-generation electron microscopy. J Mol Cell Biol 2024; 15:mjad081. [PMID: 38148118 PMCID: PMC11167312 DOI: 10.1093/jmcb/mjad081] [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: 03/22/2022] [Revised: 10/02/2022] [Accepted: 12/23/2023] [Indexed: 12/28/2023] Open
Abstract
The living body is composed of innumerable fine and complex structures. Although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these ultra-structures, the use of electron microscopy (EM) has become indispensable. However, conventional EM settings are limited to a narrow tissue area, which can bias observations. Recently, new trends in EM research have emerged, enabling coverage of far broader, nano-scale fields of view for two-dimensional wide areas and three-dimensional large volumes. Moreover, cutting-edge bioimage informatics conducted via deep learning has accelerated the quantification of complex morphological bioimages. Taken together, these technological and analytical advances have led to the comprehensive acquisition and quantification of cellular morphology, which now arises as a new omics science termed 'morphomics'.
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Affiliation(s)
- Raku Son
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Kenji Yamazawa
- Advanced Manufacturing Support Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan
| | - Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Mitsuo Suga
- Multimodal Microstructure Analysis Unit, RIKEN–JEOL Collaboration Center, Kobe 650-0047, Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
| | - Motoko Yanagita
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
- IFOM—The FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Satoshi Kume
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
- Center for Health Science Innovation, Osaka City University, Osaka 530-0011, Japan
- Osaka Electro-Communication University, Neyagawa 572-8530, Japan
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Hook JL, Bhattacharya J. The pathogenesis of influenza in intact alveoli: virion endocytosis and its effects on the lung's air-blood barrier. Front Immunol 2024; 15:1328453. [PMID: 38343548 PMCID: PMC10853445 DOI: 10.3389/fimmu.2024.1328453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
Lung infection by influenza A virus (IAV) is a major cause of global mortality from lung injury, a disease defined by widespread dysfunction of the lung's air-blood barrier. Endocytosis of IAV virions by the alveolar epithelium - the cells that determine barrier function - is central to barrier loss mechanisms. Here, we address the current understanding of the mechanistic steps that lead to endocytosis in the alveolar epithelium, with an eye to how the unique structure of lung alveoli shapes endocytic mechanisms. We highlight where future studies of alveolar interactions with IAV virions may lead to new therapeutic approaches for IAV-induced lung injury.
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Affiliation(s)
- Jaime L. Hook
- Lung Imaging Laboratory, Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jahar Bhattacharya
- Department of Medicine, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, United States
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, United States
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3
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Zhang S, Sun F, Zhu J, Qi J, Wang W, Liu Z, Li W, Liu C, Liu X, Wang N, Song X, Zhang D, Qi D, Wang X. Phillyrin ameliorates influenza a virus-induced pulmonary inflammation by antagonizing CXCR2 and inhibiting NLRP3 inflammasome activation. Virol J 2023; 20:262. [PMID: 37957672 PMCID: PMC10644626 DOI: 10.1186/s12985-023-02219-4] [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: 08/11/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
Influenza is an acute viral respiratory illness with high morbidity rates worldwide. Excessive pulmonary inflammation is the main characteristic of lethal influenza A virus (IAV) infections. Therapeutic options for managing influenza are limited to vaccines and some antiviral medications. Phillyrin is one of the major bioactive components of the Chinese herbal medicine Forsythia suspensa, which has the functions of sterilization, heat clearing and detoxification. In this work, the effect and mechanism of phillyrin on H1N1 influenza (PR8)-induced pneumonia were investigated. We reported that phillyrin (15 mg/kg) treatment after viral challenge significantly improved the weight loss, ameliorated pulmonary inflammation and inhibited the accumulation of multiple cytokines and chemokines in bronchoalveolar lavage fluid on 7 days post infection (dpi). In vitro, phillyrin suppressed influenza viral replication (Matrixprotein and nucleoprotein messenger RNA level) and reduced influenza virus-induced cytopathic effect (CPE). Furthermore,chemokine receptor CXCR2 was confirmed to be markedly inhibited by phillyrin. Surface plasmon resonance results reveal that phillyrin exhibits binding affinity to CXCR2, having a binding affinity constant (KD) value of 1.858e-5 M, suggesting that CXCR2 is a potential therapeutic target for phillyrin. Moreover, phillyrin inhibited the mRNA and protein expression levels of Caspase1, ASC and NLRP3 in the lungs of mice with H1N1-induced pneumonia.This study reveals that phillyrin ameliorates IAV-induced pulmonary inflammation by antagonizing CXCR2 and inhibiting NLRP3 inflammasome activation partly.
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Affiliation(s)
- Shanyu Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Fengzhi Sun
- Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250014, China
| | - Jinlu Zhu
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Jianhong Qi
- Department of Pharmaceutics, China Pharmaceutical University, Nanjing, 211198, China
| | - Wenjing Wang
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Ziming Liu
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Wenqian Li
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Chuanguo Liu
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Xuehuan Liu
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Nonghan Wang
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Xinyu Song
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Dan Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
- Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
- Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
| | - Dongmei Qi
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
- Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
- Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
| | - Xiaolong Wang
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
- Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
- Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
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4
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Yin L, Li Y, Zhang W, Han X, Wu Q, Xie Y, Fan J, Ma L. Detection Methods for Foodborne Viruses: Current State-of-Art and Future Perspectives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3551-3563. [PMID: 36657010 DOI: 10.1021/acs.jafc.2c06537] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Foodborne viruses have been recognized as important threats to food safety and human health. Rapid and accurate detection is one of the most crucial measures for food safety control. With the development of biology, chemistry, nanoscience, and related interdisciplines, detection strategies have been devised and advanced continuously. This review mainly focuses on the progress of detection methods for foodborne viruses. The current detection methods for foodborne viruses are summarized, including traditional electron microscopy and cultural isolation, immunoassay, molecular technology, biosensors, and newly emerging CRISPR/Cas-based detection technology. Furthermore, a comparison of the detection methods was objectively discussed. This review provides a comprehensive account of foodborne virus detection methods from fundamentals to state-of-the-art and illustrates the advantages and disadvantages of the current methods and proposes the future trends and directions for foodborne virus detection. It is hoped that this review can update current knowledge and present blueprints in order to accelerate futuristic development.
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Affiliation(s)
- Lijuan Yin
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Wenlu Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xiao Han
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Qiankun Wu
- Academy of National Food and Strategic Reserves Administration, Beijing, 100037, China
| | - Yanyan Xie
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jingjing Fan
- Beijing Kwinbon Biotechnology Co., Ltd, Beijing, 102200, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
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5
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White IJ, Burden JJ. A practical guide to starting SEM array tomography-An accessible volume EM technique. Methods Cell Biol 2023; 177:171-196. [PMID: 37451766 DOI: 10.1016/bs.mcb.2022.12.023] [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] [Indexed: 02/18/2023]
Abstract
The techniques collectively known as volume electron microscopy (vEM) each come with their own advantages and challenges, making them more or less suitable for any specific project. SEM array tomography (SEM-AT) is certainly no different in this respect. Requiring microtomy skills, and involving more data alignment post imaging, SEM-AT presents challenges to its users, nevertheless, as perhaps the most flexible, cost effective and potentially accessible vEM approach to regular EM facilities, it benefits those same users with multiple advantages due to its inherently non-destructive nature. The general principles and advantages/disadvantages of SEM-AT are described here, together with a step-by-step guide to the workflow, from block trimming, sectioning and collection on coverslips, to alignment of the high-resolution 3D dataset. With a suitable SEM/backscatter electron detector setup, and equipment readily found in an electron microscopy lab, it should be possible to begin to acquire 3D ultrastructural data. With the addition of appropriate SEM-AT imaging software, this process can be significantly enhanced to automatically image hundreds, potentially thousands, of sections. Hardware and software advances and future improvements will only make this easier, to the extent that SEM-AT could become a routine vEM technique throughout the world, rather than the privilege of a small number of experts in limited specialist facilities.
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Affiliation(s)
- Ian J White
- LMCB, University College London, London, United Kingdom
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6
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Yau E, Yang L, Chen Y, Umstead TM, Atkins H, Katz ZE, Yewdell JW, Gandhi CK, Halstead ES, Chroneos ZC. Surfactant protein A alters endosomal trafficking of influenza A virus in macrophages. Front Immunol 2023; 14:919800. [PMID: 36960051 PMCID: PMC10028185 DOI: 10.3389/fimmu.2023.919800] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 02/21/2023] [Indexed: 03/09/2023] Open
Abstract
Influenza A virus infection (IAV) often leads to acute lung injury that impairs breathing and can lead to death, with disproportionate mortality in children and the elderly. Surfactant Protein A (SP-A) is a calcium-dependent opsonin that binds a variety of pathogens to help control pulmonary infections by alveolar macrophages. Alveolar macrophages play critical roles in host resistance and susceptibility to IAV infection. The effect of SP-A on IAV infection and antiviral response of macrophages, however, is not understood. Here, we report that SP-A attenuates IAV infection in a dose-dependent manner at the level of endosomal trafficking, resulting in infection delay in a model macrophage cell line. The ability of SP-A to suppress infection was independent of its glycosylation status. Binding of SP-A to hemagglutinin did not rely on the glycosylation status or sugar binding properties of either protein. Incubation of either macrophages or IAV with SP-A slowed endocytic uptake rate of IAV. SP-A interfered with binding to cell membrane and endosomal exit of the viral genome as indicated by experiments using isolated cell membranes, an antibody recognizing a pH-sensitive conformational epitope on hemagglutinin, and microscopy. Lack of SP-A in mice enhanced IFNβ expression, viral clearance and reduced mortality from IAV infection. These findings support the idea that IAV is an opportunistic pathogen that co-opts SP-A to evade host defense by alveolar macrophages. Our study highlights novel aspects of host-pathogen interactions that may lead to better understanding of the local mechanisms that shape activation of antiviral and inflammatory responses to viral infection in the lung.
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Affiliation(s)
- Eric Yau
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Linlin Yang
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Yan Chen
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Todd M. Umstead
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Hannah Atkins
- Department of Comparative Medicine, Pennsylvania State University College of Medicine, PA, Hershey, United States
| | - Zoe E. Katz
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Jonathan W. Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Chintan K. Gandhi
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - E. Scott Halstead
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Zissis C. Chroneos
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA, United States
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA, United States
- *Correspondence: Zissis C. Chroneos,
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Chen S, Liu Y, Ge J, Yin J, Shi T, Ntambara J, Cheng Z, Chu M, Gu H. Tetrandrine Treatment May Improve Clinical Outcome in Patients with COVID-19. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58091194. [PMID: 36143871 PMCID: PMC9503147 DOI: 10.3390/medicina58091194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/23/2022] [Accepted: 08/27/2022] [Indexed: 12/02/2022]
Abstract
Background and objectives: The COVID-19 pandemic continues worldwide, and there is no effective treatment to treat it. Chinese medicine is considered the recommended treatment for COVID-19 in China. This study aimed to examine the effectiveness of tetrandrine in treating COVID-19, which is originally derived from Chinese medicine. Materials and Methods: A total of 60 patients, categorized into three types (mild, moderate, severe), from Daye Hospital of Chinese Medicine with a diagnosis of COVID-19 were included in this study. Demographics, medical history, treatment, and results were collected. We defined two main groups according to the clinical outcome between improvement and recovery. All underlying factors including clinical outcomes were assessed in the total number of COVID-19 patients and moderate-type patients. Results: In a total of 60 patients, there were significant differences in the clinical outcome underlying treatment with antibiotics, tetrandrine, and arbidol (p < 0.05). When the comparison was limited to the moderate type, treatment with tetrandrine further increased recovery rate (p = 0.007). However, the difference disappeared, and no association was indicated between the clinical outcome and the treatment with and without antibiotic (p = 0.224) and arbidol (p = 0.318) in the moderate-type patients. In all-type and moderate-type patients, tetrandrine improved the rate of improvement in cough and fatigue on day 7 (p < 0.05). Conclusions: Tetrandrine may improve clinical outcome in COVID-19 patientsand could be a promising potential natural antiviral agent for the prevention and treatment of COVID-19.
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Affiliation(s)
- Shiyin Chen
- School of Medicine, Nantong University, Nantong 226000, China
| | - Yiran Liu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong 226000, China
| | - Juan Ge
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), Nantong 226000, China
| | - Jianzhong Yin
- Department of Respiratory, Daye Hospital of Chinese Medicine, Daye 435100, China
| | - Ting Shi
- Department of Respiratory, Daye Hospital of Chinese Medicine, Daye 435100, China
| | - James Ntambara
- Department of Epidemiology, School of Public Health, Nantong University, Nantong 226000, China
| | - Zhounan Cheng
- Department of Epidemiology, School of Public Health, Nantong University, Nantong 226000, China
| | - Minjie Chu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong 226000, China
- Correspondence: (M.C.); (H.G.)
| | - Hongyan Gu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), Nantong 226000, China
- Correspondence: (M.C.); (H.G.)
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8
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Multiplex Digital Quantification of β-Lactamase Genes in Antibiotic-Resistant Bacteria by Counting Gold Nanoparticle Labels on Silicon Microchips. BIOSENSORS 2022; 12:bios12040226. [PMID: 35448287 PMCID: PMC9024738 DOI: 10.3390/bios12040226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022]
Abstract
Digital quantification based on counting of individual molecules is a promising approach for different biomedical applications due to its enhanced sensitivity. Here, we present a method for the digital detection of nucleic acids (DNA and RNA) on silicon microchips based on the counting of gold nanoparticles (GNPs) in DNA duplexes by scanning electron microscopy (SEM). Biotin-labeled DNA is hybridized with capture oligonucleotide probes immobilized on the microchips. Then biotin is revealed by a streptavidin–GNP conjugate followed by the detection of GNPs. Sharp images of each nanoparticle allow the visualization of hybridization results on a single-molecule level. The technique was shown to provide highly sensitive quantification of both short oligonucleotide and long double-strand DNA sequences up to 800 bp. The lowest limit of detection of 0.04 pM was determined for short 19-mer oligonucleotide. The method’s applicability was demonstrated for the multiplex quantification of several β-lactamase genes responsible for the development of bacterial resistance against β-lactam antibiotics. Determination of nucleic acids is effective for both specific DNA in lysates and mRNA in transcripts. The method is also characterized by high selectivity for single-nucleotide polymorphism discrimination. The proposed principle of digital quantification is a perspective for studying the mechanisms of bacterial antibiotic resistance and bacterial response to drugs.
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9
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Inhibition of the antigen-presenting ability of dendritic cells by non-structural protein 2 of influenza A virus. Vet Microbiol 2022; 267:109392. [DOI: 10.1016/j.vetmic.2022.109392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 12/18/2022]
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10
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Abstract
Since its entry into biomedical research in the first half of the twentieth century, electron microscopy has been a valuable tool for lung researchers to explore the lung's delicate ultrastructure. Among others, it proved the existence of a continuous alveolar epithelium and demonstrated the surfactant lining layer. With the establishment of serial sectioning transmission electron microscopy, as the first "volume electron microscopic" technique, electron microscopy entered the third dimension and investigations of the lung's three-dimensional ultrastructure became possible. Over the years, further techniques, ranging from electron tomography over serial block-face and focused ion beam scanning electron microscopy to array tomography became available. All techniques cover different volumes and resolutions, and, thus, different scientific questions. This review gives an overview of these techniques and their application in lung research, focusing on their fields of application and practical implementation. Furthermore, an introduction is given how the output raw data are processed and the final three-dimensional models can be generated.
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Affiliation(s)
- Jan Philipp Schneider
- Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Jan Hegermann
- Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
- Research Core Unit Electron Microscopy, Hannover Medical School, 30625 Hannover, Germany
| | - Christoph Wrede
- Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
- Research Core Unit Electron Microscopy, Hannover Medical School, 30625 Hannover, Germany
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11
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Shaga Devan K, Walther P, von Einem J, Ropinski T, A Kestler H, Read C. Improved automatic detection of herpesvirus secondary envelopment stages in electron microscopy by augmenting training data with synthetic labelled images generated by a generative adversarial network. Cell Microbiol 2020; 23:e13280. [PMID: 33073426 DOI: 10.1111/cmi.13280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/01/2020] [Accepted: 10/14/2020] [Indexed: 12/16/2022]
Abstract
Detailed analysis of secondary envelopment of the herpesvirus human cytomegalovirus (HCMV) by transmission electron microscopy (TEM) is crucial for understanding the formation of infectious virions. Here, we present a convolutional neural network (CNN) that automatically recognises cytoplasmic capsids and distinguishes between three HCMV capsid envelopment stages in TEM images. 315 TEM images containing 2,610 expert-labelled capsids of the three classes were available for CNN training. To overcome the limitation of small training datasets and thus poor CNN performance, we used a deep learning method, the generative adversarial network (GAN), to automatically increase our labelled training dataset with 500 synthetic images and thus to 9,192 labelled capsids. The synthetic TEM images were added to the ground truth dataset to train the Faster R-CNN deep learning-based object detector. Training with 315 ground truth images yielded an average precision (AP) of 53.81% for detection, whereas the addition of 500 synthetic training images increased the AP to 76.48%. This shows that generation and additional use of synthetic labelled images for detector training is an inexpensive way to improve detector performance. This work combines the gold standard of secondary envelopment research with state-of-the-art deep learning technology to speed up automatic image analysis even when large labelled training datasets are not available.
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Affiliation(s)
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Jens von Einem
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Timo Ropinski
- Institute of Media Informatics, Ulm University, Ulm, Germany
| | | | - Clarissa Read
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany.,Institute of Virology, Ulm University Medical Center, Ulm, Germany
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12
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Ozaki T, Utsumi S, Iwamoto T, Tanaka M, Tomita H, Sugano E, Ishiyama E, Ishida K. Data on mitochondrial ultrastructure of photoreceptors in pig, rabbit, and mouse retinas. Data Brief 2020; 30:105544. [PMID: 32368587 PMCID: PMC7186507 DOI: 10.1016/j.dib.2020.105544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/17/2020] [Accepted: 04/02/2020] [Indexed: 12/05/2022] Open
Abstract
Photoreceptors are one of the most energy-consuming cell types within the human body. To meet their high energy demand, photoreceptors possess a mitochondrial cluster in the inner segment of the cell. Interestingly, in several species, the inner segment of cone photoreceptors contains extremely large mitochondria that exceed 2 µm in diameter, called mega-mitochondria. We previously reported that pig retinas also contain mega-mitochondria, however, there are few reports whether mega-mitochondria are present in mammalian photoreceptors. In the present experiment, we analyzed pig, rabbit, and mouse photoreceptors under a scanning electron microscope (SEM), and compared the mitochondrial morphology. Our data showed that all three species present numerous mitochondrial clusters in the ellipsoid zone of photoreceptors, adjacent to the outer segment. In the pig retina, the inner segments of cone and rod photoreceptors were localized in different layers; consequently, we were able to distinguish them easily. Mega-mitochondria were identified only in the inner segment of cone photoreceptors. Also, mitochondria of cone photoreceptors, including mega-mitochondria, were dense cristae and high electron-densities compared to those of rod photoreceptors. In the rabbit retina, cone photoreceptors were existed within the layer of rod photoreceptor outer segment. The rod photoreceptors had a characteristic long outer segment. Cone photoreceptors had a short outer segment, and also had a thick inner segment compared to rod photoreceptors. Most of the mitochondria present in the rod photoreceptor inner segment were long and narrow, whereas mitochondria of cone photoreceptors were fragmented and short. Mega-mitochondria was not detected in rabbit retina. In the mouse retina, most of the photoreceptor cells were rod photoreceptors. Since the shape of the inner segments were very similar, we distinguished cone and rod photoreceptors based on the shape of the outer segments. Some mitochondria of both rod and cone photoreceptors were long and narrow, and there was no significant difference in mitochondrial morphology. Our data showed that mitochondrial morphology in the inner segment of photoreceptors vary among mammalian species. Although mega-mitochondria were present in pig photoreceptors, we could not observe their presence in rabbit nor mouse retinas. To our knowledge, this is a first experiment that perform the wide field observation of rabbit and mouse retina using electron microscopy, and that compare the mitochondrial morphology of photoreceptor cells in pig, rabbit and mouse.
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Key Words
- CIS, cone photoreceptor inner segment
- Cone
- Ellipsoid
- GCL, ganglion cell layer
- INL, inner nuclear layer
- IPL, inner plexiform layer
- IS, inner segment
- Inner segment
- Mitochondria
- ONL, outer nuclear layer
- OPL, outer plexiform layer
- OS, outer segment
- Photoreceptor
- RIS, rod photoreceptor inner segment
- Retina
- Rod
- SEM imaging
- SEM, scanning electron microscopy
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Affiliation(s)
- Taku Ozaki
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Shinto Utsumi
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Takeshi Iwamoto
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Makoto Tanaka
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Hiroshi Tomita
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Eriko Sugano
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Eri Ishiyama
- Technical Support Center for Life Science Research, Iwate Medical University, Morioka, Japan
| | - Kinji Ishida
- Technical Support Center for Life Science Research, Iwate Medical University, Morioka, Japan
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