1
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Dharan R, Sorkin R. Biophysical aspects of migrasome organelle formation and their diverse cellular functions. Bioessays 2024; 46:e2400051. [PMID: 38922978 DOI: 10.1002/bies.202400051] [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: 03/08/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
The transient cellular organelles known as migrasomes, which form during cell migration along retraction fibers, have emerged as a crutial factor in various fundamental cellular processes and pathologies. These membrane vesicles originate from local membrane swellings, encapsulate specific cytoplasmic content, and are eventually released to the extracellular environment or taken up by recipient cells. Migrasome biogenesis entails a sequential membrane remodeling process involving a complex interplay between various molecular factors such as tetraspanin proteins, and mechanical properties like membrane tension and bending rigidity. In this review, we summarize recent studies exploring the mechanism of migrasome formation. We emphasize how physical forces, together with molecular factors, shape migrasome biogenesis, and detail the involvement of migrasomes in various cellular processes and pathologies. A comprehensive understanding of the exact mechanism underlying migrasome formation and the identification of key molecules involved hold promise for advancing their therapeutic and diagnostic applications.
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Affiliation(s)
- Raviv Dharan
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Raya Sorkin
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
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2
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Jiao L, Luo X, Xu Y, Sun T, Lei X, Song X, Ying B. Emerging concepts of migrasome: An up-and-coming organelle from biology to the clinic. FASEB J 2024; 38:e23811. [PMID: 39031505 DOI: 10.1096/fj.202400503rr] [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: 03/06/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/22/2024]
Abstract
Since the migrasome concept was first proposed in 2015, extensive research has been conducted on these novel organelles, which grow on retracted fibers at the posterior end of migrating cells. Recently, molecular markers, biological functions, and clinical values based on the initial formation mechanism of migrasomes have emerged. Additionally, researchers are recognizing the significant role that migrasomes play in the pathological and diagnostic processes of clinical diseases. In this review, we summarize recent advances in the biology and clinical application of migrasomes and provide a comprehensive view of the prospective challenges surrounding their clinical application.
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Affiliation(s)
- Lin Jiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xinyi Luo
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yixin Xu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ting Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinxing Lei
- Department of Laboratory Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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3
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Yang R, Xiao T, Cheng Y, Li A, Qu J, Liang R, Bao S, Wang X, Wang J, Suo J, Luo Q, Dai Q. Sharing massive biomedical data at magnitudes lower bandwidth using implicit neural function. Proc Natl Acad Sci U S A 2024; 121:e2320870121. [PMID: 38959033 PMCID: PMC11252806 DOI: 10.1073/pnas.2320870121] [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: 11/28/2023] [Accepted: 05/21/2024] [Indexed: 07/04/2024] Open
Abstract
Efficient storage and sharing of massive biomedical data would open up their wide accessibility to different institutions and disciplines. However, compressors tailored for natural photos/videos are rapidly limited for biomedical data, while emerging deep learning-based methods demand huge training data and are difficult to generalize. Here, we propose to conduct Biomedical data compRession with Implicit nEural Function (BRIEF) by representing the target data with compact neural networks, which are data specific and thus have no generalization issues. Benefiting from the strong representation capability of implicit neural function, BRIEF achieves 2[Formula: see text]3 orders of magnitude compression on diverse biomedical data at significantly higher fidelity than existing techniques. Besides, BRIEF is of consistent performance across the whole data volume, and supports customized spatially varying fidelity. BRIEF's multifold advantageous features also serve reliable downstream tasks at low bandwidth. Our approach will facilitate low-bandwidth data sharing and promote collaboration and progress in the biomedical field.
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Affiliation(s)
- Runzhao Yang
- Department of Automation, Tsinghua University, Beijing100084, China
- Institute of Brain and Cognitive Sciences, Tsinghua University, Beijing100084, China
- Shanghai Artificial Intelligence Laboratory, Shanghai200232, China
| | - Tingxiong Xiao
- Department of Automation, Tsinghua University, Beijing100084, China
| | - Yuxiao Cheng
- Department of Automation, Tsinghua University, Beijing100084, China
| | - Anan Li
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan430074, China
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou215123, China
| | - Jinyuan Qu
- Department of Automation, Tsinghua University, Beijing100084, China
| | - Rui Liang
- School of Biomedical Engineering, Hainan University, Haikou570228, China
| | - Shengda Bao
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan430074, China
| | - Xiaofeng Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan430074, China
| | - Jue Wang
- Department of Automation, Tsinghua University, Beijing100084, China
| | - Jinli Suo
- Department of Automation, Tsinghua University, Beijing100084, China
- Institute of Brain and Cognitive Sciences, Tsinghua University, Beijing100084, China
- Shanghai Artificial Intelligence Laboratory, Shanghai200232, China
| | - Qingming Luo
- School of Biomedical Engineering, Hainan University, Haikou570228, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing100084, China
- Institute of Brain and Cognitive Sciences, Tsinghua University, Beijing100084, China
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4
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Jiang D, Jiao L, Li Q, Xie R, Jia H, Wang S, Chen Y, Liu S, Huang D, Zheng J, Song W, Li Y, Chen J, Li J, Ying B, Yu L. Neutrophil-derived migrasomes are an essential part of the coagulation system. Nat Cell Biol 2024; 26:1110-1123. [PMID: 38997457 PMCID: PMC11251984 DOI: 10.1038/s41556-024-01440-9] [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: 03/13/2024] [Accepted: 05/14/2024] [Indexed: 07/14/2024]
Abstract
Migrasomes are organelles that are generated by migrating cells. Here we report the key role of neutrophil-derived migrasomes in haemostasis. We found that a large number of neutrophil-derived migrasomes exist in the blood of mice and humans. Compared with neutrophil cell bodies and platelets, these migrasomes adsorb and enrich coagulation factors on the surface. Moreover, they are highly enriched with adhesion molecules, which enable them to preferentially accumulate at sites of injury, where they trigger platelet activation and clot formation. Depletion of neutrophils, or genetic reduction of the number of these migrasomes, significantly decreases platelet plug formation and impairs coagulation. These defects can be rescued by intravenous injection of purified neutrophil-derived migrasomes. Our study reveals neutrophil-derived migrasomes as a previously unrecognized essential component of the haemostasis system, which may shed light on the cause of various coagulation disorders and open therapeutic possibilities.
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Affiliation(s)
- Dong Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Lin Jiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Qing Li
- Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Renxiang Xie
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haohao Jia
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - ShiHui Wang
- State Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Yining Chen
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Siyuan Liu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Dandan Huang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiajia Zheng
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, People's Republic of China
| | - Wenhao Song
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ying Li
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - JianFeng Chen
- State Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Jinsong Li
- Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
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5
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Wang D, Yu L. Migrasome biogenesis: when biochemistry meets biophysics on membranes. Trends Biochem Sci 2024:S0968-0004(24)00147-6. [PMID: 38945731 DOI: 10.1016/j.tibs.2024.06.004] [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: 03/06/2024] [Revised: 05/17/2024] [Accepted: 06/07/2024] [Indexed: 07/02/2024]
Abstract
Migrasomes, newly identified organelles, play crucial roles in intercellular communication, contributing to organ development and angiogenesis. These vesicles, forming on retraction fibers of migrating cells, showcase a sophisticated architecture. Recent research reveals that migrasome biogenesis is a complicated and highly regulated process. This review summarizes the mechanisms governing migrasome formation, proposing a model in which biogenesis is understood through the lens of membrane microdomain assembly. It underscores the critical interplay between biochemistry and biophysics. The biogenesis unfolds in three distinct stages: nucleation, maturation, and expansion, each characterized by unique morphological, biochemical, and biophysical features. We also explore the broader implications of migrasome research in membrane biology and outline key unanswered questions that represent important directions for future investigation.
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Affiliation(s)
- Dongju Wang
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li Yu
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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6
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Jiang D, He J, Yu L. The migrasome, an organelle for cell-cell communication. Trends Cell Biol 2024:S0962-8924(24)00099-0. [PMID: 38866683 DOI: 10.1016/j.tcb.2024.05.003] [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: 03/14/2024] [Revised: 04/28/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024]
Abstract
Migrasomes, newly identified extracellular organelles produced by migrating cells, are observed widely across both in vivo and in vitro studies. These organelles, rich in signaling and bioactive molecules, are pivotal in a range of physiological functions. This opinion summarizes current understanding of migrasomes, highlighting their importance as a versatile mechanism for cell-cell communication. Furthermore, it examines their roles in health and disease and potential diagnostic and therapeutic applications, and addresses the emerging challenges and open questions in this developing field.
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Affiliation(s)
- Dong Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinzhao He
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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7
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Zhang F, Liu W, Mao Y, Yang Y, Ling C, Liu Y, Yao F, Zhen Y, Wang X, Zou M. Migrasome, a migration-dependent organelle. Front Cell Dev Biol 2024; 12:1417242. [PMID: 38903534 PMCID: PMC11187097 DOI: 10.3389/fcell.2024.1417242] [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: 04/14/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Migrasomes are organelles produced by migrating cells that form on retraction fibers and are released during cell migration. Migrasomes are involved in physiological and pathological processes such as intercellular communication, cell homeostasis maintenance, signal transduction, disease occurrence and development, and cancer metastasis. In addition, methods and techniques for studying migrasomes are constantly evolving. Here, we review the discovery, formation process, regulation, and known functions of migrasomes, summarize the commonly used specific markers of migrasomes, and the methods for observing migrasomes. Meanwhile, this review also discusses the potential applications of migrasomes in physiological processes, disease diagnosis, treatment, and prognosis, and looks forward to their wider application in biomedicine. In addition, the study of migrasomes will also reveal a new perspective on the mechanism of intercellular communication and promote the further development of life science.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Mincheng Zou
- Department of Orthopaedics, Children’s Hospital of Soochow University, Suzhou, China
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8
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High-fidelity and fast 3D imaging of subcellular dynamics in native states. Nat Biotechnol 2024:10.1038/s41587-024-02293-1. [PMID: 38834706 DOI: 10.1038/s41587-024-02293-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
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9
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Luo X, Lu Z, Jin M, Chen S, Yang J. Efficient high-resolution fluorescence projection imaging over an extended depth of field through optical hardware and deep learning optimizations. BIOMEDICAL OPTICS EXPRESS 2024; 15:3831-3847. [PMID: 38867796 PMCID: PMC11166417 DOI: 10.1364/boe.523312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/27/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024]
Abstract
Optical microscopy has witnessed notable advancements but has also become more costly and complex. Conventional wide field microscopy (WFM) has low resolution and shallow depth-of-field (DOF), which limits its applications in practical biological experiments. Recently, confocal and light sheet microscopy become major workhorses for biology that incorporate high-precision scanning to perform imaging within an extended DOF but at the sacrifice of expense, complexity, and imaging speed. Here, we propose deep focus microscopy, an efficient framework optimized both in hardware and algorithm to address the tradeoff between resolution and DOF. Our deep focus microscopy achieves large-DOF and high-resolution projection imaging by integrating a deep focus network (DFnet) into light field microscopy (LFM) setups. Based on our constructed dataset, deep focus microscopy features a significantly enhanced spatial resolution of ∼260 nm, an extended DOF of over 30 µm, and broad generalization across diverse sample structures. It also reduces the computational costs by four orders of magnitude compared to conventional LFM technologies. We demonstrate the excellent performance of deep focus microscopy in vivo, including long-term observations of cell division and migrasome formation in zebrafish embryos and mouse livers at high resolution without background contamination.
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Affiliation(s)
- Xin Luo
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Zhi Lu
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Manchang Jin
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Shuai Chen
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jingyu Yang
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
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10
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Liang L, Song X, Zhao H, Lim CT. Insights into the mechanobiology of cancer metastasis via microfluidic technologies. APL Bioeng 2024; 8:021506. [PMID: 38841688 PMCID: PMC11151435 DOI: 10.1063/5.0195389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
During cancer metastasis, cancer cells will encounter various microenvironments with diverse physical characteristics. Changes in these physical characteristics such as tension, stiffness, viscosity, compression, and fluid shear can generate biomechanical cues that affect cancer cells, dynamically influencing numerous pathophysiological mechanisms. For example, a dense extracellular matrix drives cancer cells to reorganize their cytoskeleton structures, facilitating confined migration, while this dense and restricted space also acts as a physical barrier that potentially results in nuclear rupture. Identifying these pathophysiological processes and understanding their underlying mechanobiological mechanisms can aid in the development of more effective therapeutics targeted to cancer metastasis. In this review, we outline the advances of engineering microfluidic devices in vitro and their role in replicating tumor microenvironment to mimic in vivo settings. We highlight the potential cellular mechanisms that mediate their ability to adapt to different microenvironments. Meanwhile, we also discuss some important mechanical cues that still remain challenging to replicate in current microfluidic devices in future direction. While much remains to be explored about cancer mechanobiology, we believe the developments of microfluidic devices will reveal how these physical cues impact the behaviors of cancer cells. It will be crucial in the understanding of cancer metastasis, and potentially contributing to better drug development and cancer therapy.
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Affiliation(s)
- Lanfeng Liang
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Xiao Song
- Department of Biomedical Engineering, National University of Singapore, Singapore
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Lu Z, Zuo S, Shi M, Fan J, Xie J, Xiao G, Yu L, Wu J, Dai Q. Long-term intravital subcellular imaging with confocal scanning light-field microscopy. Nat Biotechnol 2024:10.1038/s41587-024-02249-5. [PMID: 38802562 DOI: 10.1038/s41587-024-02249-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 04/17/2024] [Indexed: 05/29/2024]
Abstract
Long-term observation of subcellular dynamics in living organisms is limited by background fluorescence originating from tissue scattering or dense labeling. Existing confocal approaches face an inevitable tradeoff among parallelization, resolution and phototoxicity. Here we present confocal scanning light-field microscopy (csLFM), which integrates axially elongated line-confocal illumination with the rolling shutter in scanning light-field microscopy (sLFM). csLFM enables high-fidelity, high-speed, three-dimensional (3D) imaging at near-diffraction-limit resolution with both optical sectioning and low phototoxicity. By simultaneous 3D excitation and detection, the excitation intensity can be reduced below 1 mW mm-2, with 15-fold higher signal-to-background ratio over sLFM. We imaged subcellular dynamics over 25,000 timeframes in optically challenging environments in different species, such as migrasome delivery in mouse spleen, retractosome generation in mouse liver and 3D voltage imaging in Drosophila. Moreover, csLFM facilitates high-fidelity, large-scale neural recording with reduced crosstalk, leading to high orientation selectivity to visual stimuli, similar to two-photon microscopy, which aids understanding of neural coding mechanisms.
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Affiliation(s)
- Zhi Lu
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- Zhejiang Hehu Technology, Hangzhou, China
- Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou, China
| | - Siqing Zuo
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Minghui Shi
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiaqi Fan
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jingyu Xie
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Guihua Xiao
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
- Shanghai AI Laboratory, Shanghai, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
- Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China.
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12
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Qiao C, Zeng Y, Meng Q, Chen X, Chen H, Jiang T, Wei R, Guo J, Fu W, Lu H, Li D, Wang Y, Qiao H, Wu J, Li D, Dai Q. Zero-shot learning enables instant denoising and super-resolution in optical fluorescence microscopy. Nat Commun 2024; 15:4180. [PMID: 38755148 PMCID: PMC11099110 DOI: 10.1038/s41467-024-48575-9] [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: 10/07/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Computational super-resolution methods, including conventional analytical algorithms and deep learning models, have substantially improved optical microscopy. Among them, supervised deep neural networks have demonstrated outstanding performance, however, demanding abundant high-quality training data, which are laborious and even impractical to acquire due to the high dynamics of living cells. Here, we develop zero-shot deconvolution networks (ZS-DeconvNet) that instantly enhance the resolution of microscope images by more than 1.5-fold over the diffraction limit with 10-fold lower fluorescence than ordinary super-resolution imaging conditions, in an unsupervised manner without the need for either ground truths or additional data acquisition. We demonstrate the versatile applicability of ZS-DeconvNet on multiple imaging modalities, including total internal reflection fluorescence microscopy, three-dimensional wide-field microscopy, confocal microscopy, two-photon microscopy, lattice light-sheet microscopy, and multimodal structured illumination microscopy, which enables multi-color, long-term, super-resolution 2D/3D imaging of subcellular bioprocesses from mitotic single cells to multicellular embryos of mouse and C. elegans.
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Affiliation(s)
- Chang Qiao
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography, Tsinghua University, 100084, Beijing, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, 100010, Beijing, China
| | - Yunmin Zeng
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Quan Meng
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xingye Chen
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography, Tsinghua University, 100084, Beijing, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, 100010, Beijing, China
- Research Institute for Frontier Science, Beihang University, 100191, Beijing, China
| | - Haoyu Chen
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tao Jiang
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Rongfei Wei
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jiabao Guo
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wenfeng Fu
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Huaide Lu
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Di Li
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yuwang Wang
- Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China
| | - Hui Qiao
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography, Tsinghua University, 100084, Beijing, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, 100010, Beijing, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography, Tsinghua University, 100084, Beijing, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, 100010, Beijing, China
| | - Dong Li
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, 100084, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China.
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography, Tsinghua University, 100084, Beijing, China.
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, 100010, Beijing, China.
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13
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Deng S, Wu Y, Huang S, Yang X. Novel insights into the roles of migrasome in cancer. Discov Oncol 2024; 15:166. [PMID: 38748047 PMCID: PMC11096295 DOI: 10.1007/s12672-024-00942-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 03/18/2024] [Indexed: 05/18/2024] Open
Abstract
Cell migration, a hallmark of cancer malignancy, plays a critical role in cancers. Improperly initiated or misdirected cell migration can lead to invasive metastatic cancer. Migrasomes are newly discovered vesicular cellular organelles produced by migrating cells and depending on cell migration. Four marker proteins [NDST1 (bifunctionalheparan sulfate N-deacetylase/N-sulfotransferase 1), EOGT (Epidermal growth factor domains pecific O-linked N-acetylglucosaminetransferase), CPQ (carboxypeptidase Q), and PIGK (phosphatidylinositol glycan anchor biosynthesis, class K)] of migrasomes were successfully identified. There are three marker proteins (NDST1, PIGK, and EOGT) of migrasome expressed in cancer. In this review, we will discuss the process of migrasome discovery, the formation of migrasome, the possible functions of migrasome, and the differences between migrasomes and exosomes, especially, the biological functions of migrasome marker proteins in cancer, and discuss some possible roles of migrasomes in cancer. We speculate that migrasomes and migracytosis can play key roles in regulating the development of cancer.
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Affiliation(s)
- Sijun Deng
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang , 421001, Hunan, People's Republic of China
| | - Yiwen Wu
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang , 421001, Hunan, People's Republic of China
| | - Sheng Huang
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang , 421001, Hunan, People's Republic of China
| | - Xiaoyan Yang
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang , 421001, Hunan, People's Republic of China.
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14
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Huang Y, Yu L. Seeing is believing: observation of migrasomes. BIOPHYSICS REPORTS 2024; 10:67-81. [PMID: 38774353 PMCID: PMC11103717 DOI: 10.52601/bpr.2023.230024] [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: 10/22/2023] [Accepted: 12/29/2023] [Indexed: 05/24/2024] Open
Abstract
Migrasomes are a novel type of cell organelle that form on the retraction fibers at the rear of migrating cells. In recent years, numerous studies have unveiled the mechanisms of migrasome formation and have highlighted significant roles of migrasomes in both physiological and pathological processes. Building upon the strategies outlined in published works and our own research experiences, we have compiled a comprehensive set of protocols for observing migrasomes. These step-by-step instructions encompass various aspects such as cell culture, labeling, imaging, in vitro reconstitution, and statistical analysis. We believe that these protocols serve as a valuable resource for researchers exploring migrasome biology.
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Affiliation(s)
- Yuwei Huang
- School of Basic Medical Sciences, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an 710049, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
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15
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Ortmann W, Such A, Kolaczkowska E. Impact of microparticles released during murine systemic inflammation on macrophage activity and reactive nitrogen species regulation. Immunol Res 2024; 72:299-319. [PMID: 38008825 PMCID: PMC11031483 DOI: 10.1007/s12026-023-09436-7] [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: 04/06/2023] [Accepted: 11/13/2023] [Indexed: 11/28/2023]
Abstract
Microparticles (MPs) packaged with numerous bioactive molecules are essential vehicles in cellular communication in various pathological conditions, including systemic inflammation, Whereas MPs are studied mostly upon isolation, their detection in vivo is limited. Impact of MPs might depend on target cell type and cargo they carry; thus herein, we aimed at verifying MPs' impact on macrophages. Unlike neutrophils, monocytes/macrophages are rather inactive during sepsis, and we hypothesized this might be at least partially controlled by MPs. For the above reasons, we focused on the detection of MPs with intravital microscopy (IVM) and report the presence of putative neutrophil-derived MPs in the vasculature of cremaster muscle of endotoxemic mice. Subsequently, we characterized MPs isolated not only from their blood but also from the peritoneal cavity and observed differences in their size, concentration, and cargo. Such MPs were then used to study their impact on RAW 264.7 macrophage cell line performance (cell viability/activity, cytokines, oxygen, and nitrogen reactive species). Addition of MPs to macrophages with or without co-stimulation with lipopolysaccharide did not affect respiratory burst, somewhat decreased mitochondrial activity but increased inducible nitric oxide synthase (iNOS) expression, and NO production especially in case of plasma-derived MPs. The latter MPs carried more iNOS-controlling ceruloplasmin than those discharged into the peritoneal cavity. We conclude that MPs can be detected in vivo with IVM and their cellular origin identified. They are heterogeneous in nature depending on the site of their release. Consequently, microparticles released during systemic inflammation to various body compartments differentially affect macrophages.
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Affiliation(s)
- Weronika Ortmann
- Laboratory of Experimental Hematology, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9 Street, 30-387, Krakow, Poland
| | - Anna Such
- Laboratory of Experimental Hematology, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9 Street, 30-387, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Elzbieta Kolaczkowska
- Laboratory of Experimental Hematology, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9 Street, 30-387, Krakow, Poland.
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16
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Chen S, Lu Z, Zhao Y, Xia L, Liu C, Zuo S, Jin M, Jia H, Li S, Zhang S, Yang B, Wang Z, Li J, Wang F, Yang C. Myeloid-Mas Signaling Modulates Pathogenic Crosstalk among MYC +CD63 + Endothelial Cells, MMP12 + Macrophages, and Monocytes in Acetaminophen-Induced Liver Injury. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306066. [PMID: 38350725 PMCID: PMC11040347 DOI: 10.1002/advs.202306066] [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: 08/25/2023] [Revised: 01/17/2024] [Indexed: 02/15/2024]
Abstract
Acetaminophen overdose is a leading cause of acute liver failure (ALF). Despite the pivotal role of the inflammatory microenvironment in the progression of advanced acetaminophen-induced liver injury (AILI), a comprehensive understanding of the underlying cellular interactions and molecular mechanisms remains elusive. Mas is a G protein-coupled receptor highly expressed by myeloid cells; however, its role in the AILI microenvironment remains to be elucidated. A multidimensional approach, including single-cell RNA sequencing, spatial transcriptomics, and hour-long intravital imaging, is employed to characterize the microenvironment in Mas1 deficient mice at the systemic and cell-specific levels. The characteristic landscape of mouse AILI models involves reciprocal cellular communication among MYC+CD63+ endothelial cells, MMP12+ macrophages, and monocytes, which is maintained by enhanced glycolysis and the NF-κB/TNF-α signaling pathway due to myeloid-Mas deficiency. Importantly, the pathogenic microenvironment is delineated in samples obtained from patients with ALF, demonstrating its clinical relevance. In summary, these findings greatly enhance the understanding of the microenvironment in advanced AILI and offer potential avenues for patient stratification and identification of novel therapeutic targets.
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Affiliation(s)
- Shuai Chen
- Department of Gastroenterology and HepatologyTongji Hospital, School of Medicine, Tongji UniversityShanghai200092China
| | - Zhi Lu
- Department of AutomationTsinghua UniversityBeijing100084China
- Institute for Brain and Cognitive SciencesTsinghua UniversityBeijing100084China
| | - Yudong Zhao
- Department of Liver Surgery, Renji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Lu Xia
- Department of Gastroenterology and HepatologyTongji Hospital, School of Medicine, Tongji UniversityShanghai200092China
| | - Chun Liu
- Department of Gastroenterology and HepatologyTongji Hospital, School of Medicine, Tongji UniversityShanghai200092China
| | - Siqing Zuo
- Department of AutomationTsinghua UniversityBeijing100084China
- Institute for Brain and Cognitive SciencesTsinghua UniversityBeijing100084China
| | - Manchang Jin
- Institute for Brain and Cognitive SciencesTsinghua UniversityBeijing100084China
- School of Electrical and Information EngineeringTianjin UniversityTianjin300072China
| | - Haoyu Jia
- Department of Gastroenterology and HepatologyTongji Hospital, School of Medicine, Tongji UniversityShanghai200092China
| | - Shanshan Li
- Department of Gastroenterology and HepatologyTongji Hospital, School of Medicine, Tongji UniversityShanghai200092China
| | - Shuo Zhang
- Department of Gastroenterology and HepatologyTongji Hospital, School of Medicine, Tongji UniversityShanghai200092China
| | - Bo Yang
- Department of Gastroenterology and HepatologyTongji Hospital, School of Medicine, Tongji UniversityShanghai200092China
| | - Zhijing Wang
- Department of Gastroenterology and HepatologyTongji Hospital, School of Medicine, Tongji UniversityShanghai200092China
| | - Jing Li
- Department of Gastroenterology and HepatologyTongji Hospital, School of Medicine, Tongji UniversityShanghai200092China
| | - Fei Wang
- Division of GastroenterologySeventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhen518107China
| | - Changqing Yang
- Department of Gastroenterology and HepatologyTongji Hospital, School of Medicine, Tongji UniversityShanghai200092China
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17
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Zhang Y, Gu S, Du J, Huang G, Shi J, Lu X, Wang J, Yang W, Guo X, Zhao C. Plant microphenotype: from innovative imaging to computational analysis. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:802-818. [PMID: 38217351 PMCID: PMC10955502 DOI: 10.1111/pbi.14244] [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: 03/10/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 01/15/2024]
Abstract
The microphenotype plays a key role in bridging the gap between the genotype and the complex macro phenotype. In this article, we review the advances in data acquisition and the intelligent analysis of plant microphenotyping and present applications of microphenotyping in plant science over the past two decades. We then point out several challenges in this field and suggest that cross-scale image acquisition strategies, powerful artificial intelligence algorithms, advanced genetic analysis, and computational phenotyping need to be established and performed to better understand interactions among genotype, environment, and management. Microphenotyping has entered the era of Microphenotyping 3.0 and will largely advance functional genomics and plant science.
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Affiliation(s)
- Ying Zhang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shenghao Gu
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianjun Du
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Guanmin Huang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jiawei Shi
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xianju Lu
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinglu Wang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Guo
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunjiang Zhao
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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18
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Hua X, Han K, Mandracchia B, Radmand A, Liu W, Kim H, Yuan Z, Ehrlich SM, Li K, Zheng C, Son J, Silva Trenkle AD, Kwong GA, Zhu C, Dahlman JE, Jia S. Light-field flow cytometry for high-resolution, volumetric and multiparametric 3D single-cell analysis. Nat Commun 2024; 15:1975. [PMID: 38438356 PMCID: PMC10912605 DOI: 10.1038/s41467-024-46250-7] [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: 04/19/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024] Open
Abstract
Imaging flow cytometry (IFC) combines flow cytometry and fluorescence microscopy to enable high-throughput, multiparametric single-cell analysis with rich spatial details. However, current IFC techniques remain limited in their ability to reveal subcellular information with a high 3D resolution, throughput, sensitivity, and instrumental simplicity. In this study, we introduce a light-field flow cytometer (LFC), an IFC system capable of high-content, single-shot, and multi-color acquisition of up to 5,750 cells per second with a near-diffraction-limited resolution of 400-600 nm in all three dimensions. The LFC system integrates optical, microfluidic, and computational strategies to facilitate the volumetric visualization of various 3D subcellular characteristics through convenient access to commonly used epi-fluorescence platforms. We demonstrate the effectiveness of LFC in assaying, analyzing, and enumerating intricate subcellular morphology, function, and heterogeneity using various phantoms and biological specimens. The advancement offered by the LFC system presents a promising methodological pathway for broad cell biological and translational discoveries, with the potential for widespread adoption in biomedical research.
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Affiliation(s)
- Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Keyi Han
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Afsane Radmand
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Chemical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hyejin Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Zhou Yuan
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Samuel M Ehrlich
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kaitao Li
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Corey Zheng
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jeonghwan Son
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Aaron D Silva Trenkle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - James E Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA.
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19
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Ortmann W, Such A, Cichon I, Baj-Krzyworzeka M, Weglarczyk K, Kolaczkowska E. Large extracellular vesicle (EV) and neutrophil extracellular trap (NET) interaction captured in vivo during systemic inflammation. Sci Rep 2024; 14:4680. [PMID: 38409254 PMCID: PMC10897202 DOI: 10.1038/s41598-024-55081-x] [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: 11/17/2023] [Accepted: 02/19/2024] [Indexed: 02/28/2024] Open
Abstract
Extracellular vesicles (EVs) and neutrophil extracellular traps (NETs) are pivotal bioactive structures involved in various processes including inflammation. Herein we report the interactions between EVs and NETs during murine endotoxemia studied in situ directly in the vasculature (cremaster muscle, liver sinusoids) using intravital microscopy (IVM). We captured NETs and EV release in real time by both non- and polarized neutrophils in liver but not in cremaster vasculature. When comparing numbers of circulating EVs of various origin (nanoparticle tracking analysis-NTA, flow cytometry) with those interacting with endothelium and NETs (IVM) we observed that whereas platelet and monocyte/macrophage-derived EVs dominate in blood and peritoneal lavage, respectively, mostly neutrophil-derived EVs interact with the vascular lining, NETs and leukocytes. Despite the interaction, NETs do not affect EV formation as NET release inhibition did not alter EV release. However, EVs inhibit NETs formation and in particular, erythrocyte-derived EVs downregulate NET release and this effect is mediated via Siglec-E-dependent interactions with neutrophils. Overall, we report that EVs are present in NETs in vivo and they do modulate their release but the process in not bidirectional. Moreover, EVs isolated from body fluids might not reflect their importance in direct endothelial- and leukocyte-related interactions.
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Affiliation(s)
- Weronika Ortmann
- Department of Experimental Hematology, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9 Str, 30-387, Krakow, Poland
| | - Anna Such
- Department of Experimental Hematology, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9 Str, 30-387, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Iwona Cichon
- Department of Experimental Hematology, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9 Str, 30-387, Krakow, Poland
| | - Monika Baj-Krzyworzeka
- Department of Clinical Immunology, Jagiellonian University Medical College, Wielicka 265 Str, 30-663, Krakow, Poland
| | - Kazimierz Weglarczyk
- Department of Clinical Immunology, Jagiellonian University Medical College, Wielicka 265 Str, 30-663, Krakow, Poland
| | - Elzbieta Kolaczkowska
- Department of Experimental Hematology, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9 Str, 30-387, Krakow, Poland.
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20
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Zhang S, Song W, Hua Z, Du J, Lucena RB, Wang X, Zhang C, Yang X. Overview of T-2 Toxin Enterotoxicity: From Toxic Mechanisms and Detoxification to Future Perspectives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3314-3324. [PMID: 38331717 DOI: 10.1021/acs.jafc.3c09416] [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: 02/10/2024]
Abstract
Fusarium species produce a secondary metabolite known as T-2 toxin, which is the primary and most harmful toxin found in type A trichothecenes. T-2 toxin is widely found in food and grain-based animal feed and endangers the health of both humans and animals. T-2 toxin exposure in humans and animals occurs primarily through food administration; therefore, the first organ that T-2 toxin targets is the gut. In this overview, the research progress, toxicity mechanism, and detoxification of the toxin T-2 were reviewed, and future research directions were proposed. T-2 toxin damages the intestinal mucosa and destroys intestinal structure and intestinal barrier function; furthermore, T-2 toxin disrupts the intestinal microbiota, causes intestinal flora disorders, affects normal intestinal metabolic function, and kills intestinal epidermal cells by inducing oxidative stress, inflammatory responses, and apoptosis. The primary harmful mechanism of T-2 toxin in the intestine is oxidative stress. Currently, selenium and plant extracts are mainly used to exert antioxidant effects to alleviate the enterotoxicity of T-2 toxin. In future studies, the use of genomic techniques to find upstream signaling molecules associated with T-2 enterotoxin toxicity will provide new ideas for the prevention of this toxicity. The purpose of this paper is to review the progress of research on the intestinal toxicity of T-2 toxin and propose new research directions for the prevention and treatment of T-2 toxin toxicity.
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Affiliation(s)
- Shanshan Zhang
- College of Veterinary Medicine Henan Agricultural University No.15 Longzihu University Park, Zhengdong New District, Zhengzhou 450046, Henan, P. R. China
- Key Laboratory of Quality and Safety Control of Poultry Products, Ministry of Agriculture and Rural Affairs, Zhengzhou 450000, Henan, P. R. China
| | - Wenxi Song
- College of Veterinary Medicine Henan Agricultural University No.15 Longzihu University Park, Zhengdong New District, Zhengzhou 450046, Henan, P. R. China
| | - Zeao Hua
- College of Veterinary Medicine Henan Agricultural University No.15 Longzihu University Park, Zhengdong New District, Zhengzhou 450046, Henan, P. R. China
| | - Juanjuan Du
- College of Veterinary Medicine Henan Agricultural University No.15 Longzihu University Park, Zhengdong New District, Zhengzhou 450046, Henan, P. R. China
| | - Ricardo Barbosa Lucena
- Laboratory of Veterinary Pathology, Department of Veterinary Sciences, Federal University of Paraiba, Areia 58397-000, Paraiba Brazil
| | - Xuebing Wang
- College of Veterinary Medicine Henan Agricultural University No.15 Longzihu University Park, Zhengdong New District, Zhengzhou 450046, Henan, P. R. China
| | - Cong Zhang
- College of Veterinary Medicine Henan Agricultural University No.15 Longzihu University Park, Zhengdong New District, Zhengzhou 450046, Henan, P. R. China
- Key Laboratory of Quality and Safety Control of Poultry Products, Ministry of Agriculture and Rural Affairs, Zhengzhou 450000, Henan, P. R. China
| | - Xu Yang
- College of Veterinary Medicine Henan Agricultural University No.15 Longzihu University Park, Zhengdong New District, Zhengzhou 450046, Henan, P. R. China
- Key Laboratory of Quality and Safety Control of Poultry Products, Ministry of Agriculture and Rural Affairs, Zhengzhou 450000, Henan, P. R. China
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21
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Wang Y, Wang B, Wang P, Hua Z, Zhang S, Wang X, Yang X, Zhang C. Review of neurotoxicity of T-2 toxin. Mycotoxin Res 2024; 40:85-95. [PMID: 38217761 DOI: 10.1007/s12550-024-00518-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
T-2 toxin is a representative trichothecene that is widely detected in corn, wheat and other grain feeds. T-2 toxin has stable physical and chemical properties, making it difficult to remove from food and feed. Hence, T-2 toxin has become an unavoidable pollutant in food for humans and animals. T-2 toxin can enter brain tissue by crossing the blood-brain barrier and leads to congestion, swelling and even apoptosis of neurons. T-2 toxin poisoning can directly lead to clinical symptoms (anti-feeding reaction and decline of learning and memory function in humans and animals). Maternal T-2 toxin exposure also exerted toxic effects on the central nervous system of offspring. Oxidative stress is the core neurotoxicity mechanism underlying T-2 toxin poison. Oxidative stress-mediated apoptosis, mitochondrial oxidative damage and inflammation are all involved in the neurotoxicity induced by T-2 toxin. Thus, alleviating oxidative stress has become a potential target for relieving the neurotoxicity induced by T-2 toxin. Future efforts should be devoted to revealing the neurotoxic molecular mechanism of T-2 toxin and exploring effective therapeutic drugs to alleviate T-2 toxin-induced neurotoxicity.
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Affiliation(s)
- Youshuang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Bo Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Peilin Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Zeao Hua
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Shanshan Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Xuebing Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Xu Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
- Key Laboratory of Quality and Safety Control of Poultry Products, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Cong Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
- Key Laboratory of Quality and Safety Control of Poultry Products, Ministry of Agriculture and Rural Affairs, Zhengzhou, China.
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22
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Shi W, Quan H, Kong L. High-resolution 3D imaging in light-field microscopy through Stokes matrices and data fusion. OPTICS EXPRESS 2024; 32:3710-3722. [PMID: 38297586 DOI: 10.1364/oe.510728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
The trade-off between the lateral and vertical resolution has long posed challenges to the efficient and widespread application of Fourier light-field microscopy, a highly scalable 3D imaging tool. Although existing methods for resolution enhancement can improve the measurement result to a certain extent, they come with limitations in terms of accuracy and applicable specimen types. To address these problems, this paper proposed a resolution enhancement scheme utilizing data fusion of polarization Stokes vectors and light-field information for Fourier light-field microscopy system. By introducing the surface normal vector information obtained from polarization measurement and integrating it with the light-field 3D point cloud data, 3D reconstruction results accuracy is highly improved in axial direction. Experimental results with a Fourier light-field 3D imaging microscope demonstrated a substantial enhancement of vertical resolution with a depth resolution to depth of field ratio of 0.19%. This represented approximately 44 times the improvement compared to the theoretical ratio before data fusion, enabling the system to access more detailed information with finer measurement accuracy for test samples. This work not only provides a feasible solution for breaking the limitations imposed by traditional light-field microscope hardware configurations but also offers superior 3D measurement approach in a more cost-effective and practical manner.
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23
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Chai Y, Qi K, Wu Y, Li D, Tan G, Guo Y, Chu J, Mu Y, Shen C, Wen Q. All-optical interrogation of brain-wide activity in freely swimming larval zebrafish. iScience 2024; 27:108385. [PMID: 38205255 PMCID: PMC10776927 DOI: 10.1016/j.isci.2023.108385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/22/2023] [Accepted: 10/30/2023] [Indexed: 01/12/2024] Open
Abstract
We introduce an all-optical technique that enables volumetric imaging of brain-wide calcium activity and targeted optogenetic stimulation of specific brain regions in unrestrained larval zebrafish. The system consists of three main components: a 3D tracking module, a dual-color fluorescence imaging module, and a real-time activity manipulation module. Our approach uses a sensitive genetically encoded calcium indicator in combination with a long Stokes shift red fluorescence protein as a reference channel, allowing the extraction of Ca2+ activity from signals contaminated by motion artifacts. The method also incorporates rapid 3D image reconstruction and registration, facilitating real-time selective optogenetic stimulation of different regions of the brain. By demonstrating that selective light activation of the midbrain regions in larval zebrafish could reliably trigger biased turning behavior and changes of brain-wide neural activity, we present a valuable tool for investigating the causal relationship between distributed neural circuit dynamics and naturalistic behavior.
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Affiliation(s)
- Yuming Chai
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Kexin Qi
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Yubin Wu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Daguang Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Guodong Tan
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Yuqi Guo
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology and Center for Biomedical Optics and Molecular Imaging, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jun Chu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology and Center for Biomedical Optics and Molecular Imaging, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yu Mu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Chen Shen
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Quan Wen
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
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24
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Zhang C, Wang Y, Zhang X, Zhang K, Chen F, Fan J, Wang X, Yang X. Maintaining the Mitochondrial Quality Control System Was a Key Event of Tanshinone IIA against Deoxynivalenol-Induced Intestinal Toxicity. Antioxidants (Basel) 2024; 13:121. [PMID: 38247545 PMCID: PMC10812604 DOI: 10.3390/antiox13010121] [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: 12/28/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Deoxynivalenol (DON) is the one of the most common mycotoxins, widely detected in various original foods and processed foods. Tanshinone IIA (Tan IIA) is a fat-soluble diterpene quinone extracted from Salvia miltiorrhiza Bunge, which has multi-biological functions and pharmacological effects. However, whether Tan IIA has a protective effect against DON-induced intestinal toxicity is unknown. In this study, the results showed Tan IIA treatment could attenuate DON-induced IPEC-J2 cell death. DON increased oxidation product accumulation, decreased antioxidant ability and disrupted barrier function, while Tan IIA reversed DON-induced barrier function impairment and oxidative stress. Furthermore, Tan IIA dramatically improved mitochondrial function via mitochondrial quality control. Tan IIA could upregulate mitochondrial biogenesis and mitochondrial fusion as well as downregulate mitochondrial fission and mitochondrial unfolded protein response. In addition, Tan IIA significantly attenuated mitophagy caused by DON. Collectively, Tan IIA presented a potential protective effect against DON toxicity and the underlying mechanisms were involved in mitochondrial quality control-mediated mitophagy.
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Affiliation(s)
- Cong Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (C.Z.); (Y.W.); (X.Z.); (K.Z.); (F.C.); (J.F.); (X.W.)
- Key Laboratory of Quality and Safety Control of Poultry Products, Ministry of Agriculture and Rural Affairs, Zhengzhou 450002, China
| | - Youshuang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (C.Z.); (Y.W.); (X.Z.); (K.Z.); (F.C.); (J.F.); (X.W.)
| | - Xinyu Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (C.Z.); (Y.W.); (X.Z.); (K.Z.); (F.C.); (J.F.); (X.W.)
| | - Kefei Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (C.Z.); (Y.W.); (X.Z.); (K.Z.); (F.C.); (J.F.); (X.W.)
| | - Fengjuan Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (C.Z.); (Y.W.); (X.Z.); (K.Z.); (F.C.); (J.F.); (X.W.)
| | - Jiayan Fan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (C.Z.); (Y.W.); (X.Z.); (K.Z.); (F.C.); (J.F.); (X.W.)
| | - Xuebing Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (C.Z.); (Y.W.); (X.Z.); (K.Z.); (F.C.); (J.F.); (X.W.)
| | - Xu Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (C.Z.); (Y.W.); (X.Z.); (K.Z.); (F.C.); (J.F.); (X.W.)
- Key Laboratory of Quality and Safety Control of Poultry Products, Ministry of Agriculture and Rural Affairs, Zhengzhou 450002, China
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25
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Zhang G, Li X, Zhang Y, Han X, Li X, Yu J, Liu B, Wu J, Yu L, Dai Q. Bio-friendly long-term subcellular dynamic recording by self-supervised image enhancement microscopy. Nat Methods 2023; 20:1957-1970. [PMID: 37957429 PMCID: PMC10703694 DOI: 10.1038/s41592-023-02058-9] [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: 10/21/2022] [Accepted: 09/29/2023] [Indexed: 11/15/2023]
Abstract
Fluorescence microscopy has become an indispensable tool for revealing the dynamic regulation of cells and organelles. However, stochastic noise inherently restricts optical interrogation quality and exacerbates observation fidelity when balancing the joint demands of high frame rate, long-term recording and low phototoxicity. Here we propose DeepSeMi, a self-supervised-learning-based denoising framework capable of increasing signal-to-noise ratio by over 12 dB across various conditions. With the introduction of newly designed eccentric blind-spot convolution filters, DeepSeMi effectively denoises images with no loss of spatiotemporal resolution. In combination with confocal microscopy, DeepSeMi allows for recording organelle interactions in four colors at high frame rates across tens of thousands of frames, monitoring migrasomes and retractosomes over a half day, and imaging ultra-phototoxicity-sensitive Dictyostelium cells over thousands of frames. Through comprehensive validations across various samples and instruments, we prove DeepSeMi to be a versatile and biocompatible tool for breaking the shot-noise limit.
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Affiliation(s)
- Guoxun Zhang
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Xiaopeng Li
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanlong Zhang
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Xiaofei Han
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Xinyang Li
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jinqiang Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Boqi Liu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Shanghai AI Laboratory, Shanghai, China.
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
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26
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Li X, Hu X, Chen X, Fan J, Zhao Z, Wu J, Wang H, Dai Q. Spatial redundancy transformer for self-supervised fluorescence image denoising. NATURE COMPUTATIONAL SCIENCE 2023; 3:1067-1080. [PMID: 38177722 PMCID: PMC10766531 DOI: 10.1038/s43588-023-00568-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
Fluorescence imaging with high signal-to-noise ratios has become the foundation of accurate visualization and analysis of biological phenomena. However, the inevitable noise poses a formidable challenge to imaging sensitivity. Here we provide the spatial redundancy denoising transformer (SRDTrans) to remove noise from fluorescence images in a self-supervised manner. First, a sampling strategy based on spatial redundancy is proposed to extract adjacent orthogonal training pairs, which eliminates the dependence on high imaging speed. Second, we designed a lightweight spatiotemporal transformer architecture to capture long-range dependencies and high-resolution features at low computational cost. SRDTrans can restore high-frequency information without producing oversmoothed structures and distorted fluorescence traces. Finally, we demonstrate the state-of-the-art denoising performance of SRDTrans on single-molecule localization microscopy and two-photon volumetric calcium imaging. SRDTrans does not contain any assumptions about the imaging process and the sample, thus can be easily extended to various imaging modalities and biological applications.
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Affiliation(s)
- Xinyang Li
- Department of Automation, Tsinghua University, Beijing, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Xiaowan Hu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xingye Chen
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Research Institute for Frontier Science, Beihang University, Beijing, China
| | - Jiaqi Fan
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Department of Electronic Engineering, Tsinghua University, Beijing, China
| | - Zhifeng Zhao
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of Multi-dimension and Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
| | - Haoqian Wang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
- The Shenzhen Institute of Future Media Technology, Shenzhen, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of Multi-dimension and Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
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27
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Zheng S, Koyama M, Mertz J. Multiplane HiLo microscopy with speckle illumination and non-local means denoising. JOURNAL OF BIOMEDICAL OPTICS 2023; 28:116502. [PMID: 38078150 PMCID: PMC10704089 DOI: 10.1117/1.jbo.28.11.116502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/27/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
Significance HiLo microscopy synthesizes an optically sectioned image from two images, one obtained with uniform and another with patterned illumination, such as laser speckle. Speckle-based HiLo has the advantage of being robust to aberrations but is susceptible to residual speckle noise that is difficult to control. We present a computational method to reduce this residual noise without undermining resolution. In addition, we improve the versatility of HiLo microscopy by enabling simultaneous multiplane imaging (here nine planes). Aim Our goal is to perform fast, high-contrast, multiplane imaging with a conventional camera-based fluorescence microscope. Approach Multiplane HiLo imaging is achieved with the use of a single camera and z-splitter prism. Speckle noise reduction is based on the application of a non-local means (NLM) denoising method to perform ensemble averaging of speckle grains. Results We demonstrate the capabilities of multiplane HiLo with NLM denoising both with synthesized data and by imaging cardiac and brain activity in zebrafish larvae at 40 Hz frame rates. Conclusions Multiplane HiLo microscopy aided by NLM denoising provides a simple tool for fast optically sectioned volumetric imaging that can be of general utility for fluorescence imaging applications.
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Affiliation(s)
- Shuqi Zheng
- Boston University, Department of Electrical and Computer Engineering, Boston, Massachusetts, United States
| | - Minoru Koyama
- University of Toronto, Department of Cell and Systems Biology, Scarborough, Ontario, Canada
| | - Jerome Mertz
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
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28
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Zhang X, Yao L, Meng Y, Li B, Yang Y, Gao F. Migrasome: a new functional extracellular vesicle. Cell Death Discov 2023; 9:381. [PMID: 37852963 PMCID: PMC10584828 DOI: 10.1038/s41420-023-01673-x] [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: 05/22/2023] [Revised: 09/21/2023] [Accepted: 10/03/2023] [Indexed: 10/20/2023] Open
Abstract
Migrasome is a novel cellular organelle produced during cell migration, and its biogenesis depends on the migration process. It is generated in a variety of cells such as immune cells, metastatic tumor cells, other special functional cells like podocytes and cells in developing organisms. It plays important roles in various fields especially in the information exchange between cells. The discovery of migrasome, as an important supplement to the extracellular vesicle system, provides new mechanisms and targets for comprehending various biological or pathological processes. In this article, we will review the discovery, structure, distribution, detection, biogenesis, and removal of migrasomes and mainly focus on summarizing its biological functions in cell-to-cell communication, homeostatic maintenance, embryonic development and multiple diseases. This review also creates prospects for the possible research directions and clinical applications of migrasomes in the future.
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Affiliation(s)
- Xide Zhang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 200433, Shanghai, P. R. China
| | - Liuhuan Yao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 200433, Shanghai, P. R. China
| | - Yuanyuan Meng
- Naval Medical University, Department of Traditional Chinese Medicine, Affiliated Hospital 1, 200433, Shanghai, P. R. China
| | - Bailong Li
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 200433, Shanghai, P. R. China.
| | - Yanyong Yang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 200433, Shanghai, P. R. China.
| | - Fu Gao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 200433, Shanghai, P. R. China.
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29
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Jiang D, Li Y, Yu L. Detection, Purification, Characterization, and Manipulation of Migrasomes. Curr Protoc 2023; 3:e856. [PMID: 37540780 DOI: 10.1002/cpz1.856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
Migrasomes are newly discovered cellular organelles, first described in 2015, that are formed by migrating cells. During migration, cells leave behind long membrane tethers called retraction fibers. Numerous micrometer-scale vesicles grow from the tips or junctions of these fibers, which we have named migrasomes. Migrasomes play important roles in various physiological processes, including releasing signaling factors to ensure organ morphogenesis during zebrafish embryo development, transferring mRNAs among cells, disposing of damaged mitochondria from the cell to maintain cell homeostasis, and secreting pro-angiogenic molecules to promote angiogenesis during chicken embryo development. Migrasomes are beginning to attract the attention of researchers in multiple fields. Here, we summarize the most commonly used protocols for migrasome detection using fluorescence microscopy imaging, purification through density-gradient centrifugation, characterization using electron microscopy (EM) imaging and biochemical analysis, and manipulation of migrasomes by targeting integrins and tetraspanins. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Detection and observation of migrasomes by fluorescence microscopy imaging Basic Protocol 2: Purification of migrasomes from cultured cell lines and embryos by density-gradient centrifugation Basic Protocol 3: Characterization of migrasomes by electron microscopy imaging and biochemical analysis.
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Affiliation(s)
- Dong Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ying Li
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
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30
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Zhang Y, Song X, Xie J, Hu J, Chen J, Li X, Zhang H, Zhou Q, Yuan L, Kong C, Shen Y, Wu J, Fang L, Dai Q. Large depth-of-field ultra-compact microscope by progressive optimization and deep learning. Nat Commun 2023; 14:4118. [PMID: 37433856 DOI: 10.1038/s41467-023-39860-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/28/2023] [Indexed: 07/13/2023] Open
Abstract
The optical microscope is customarily an instrument of substantial size and expense but limited performance. Here we report an integrated microscope that achieves optical performance beyond a commercial microscope with a 5×, NA 0.1 objective but only at 0.15 cm3 and 0.5 g, whose size is five orders of magnitude smaller than that of a conventional microscope. To achieve this, a progressive optimization pipeline is proposed which systematically optimizes both aspherical lenses and diffractive optical elements with over 30 times memory reduction compared to the end-to-end optimization. By designing a simulation-supervision deep neural network for spatially varying deconvolution during optical design, we accomplish over 10 times improvement in the depth-of-field compared to traditional microscopes with great generalization in a wide variety of samples. To show the unique advantages, the integrated microscope is equipped in a cell phone without any accessories for the application of portable diagnostics. We believe our method provides a new framework for the design of miniaturized high-performance imaging systems by integrating aspherical optics, computational optics, and deep learning.
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Affiliation(s)
- Yuanlong Zhang
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, 100084, Beijing, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, 100084, Beijing, China
| | - Xiaofei Song
- Tsinghua Shenzhen International Graduate School, Tsinghua University, 518055, Shenzhen, China
| | - Jiachen Xie
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, 100084, Beijing, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, 100084, Beijing, China
| | - Jing Hu
- State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, 310027, Hangzhou, China
| | - Jiawei Chen
- OPPO Research Institute, 518101, Shenzhen, China
| | - Xiang Li
- OPPO Research Institute, 518101, Shenzhen, China
| | - Haiyu Zhang
- OPPO Research Institute, 518101, Shenzhen, China
| | - Qiqun Zhou
- OPPO Research Institute, 518101, Shenzhen, China
| | - Lekang Yuan
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, 518055, Shenzhen, China
| | - Chui Kong
- School of Information Science and Technology, Fudan University, 200433, Shanghai, China
| | - Yibing Shen
- State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, 310027, Hangzhou, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, 100084, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China.
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, 100084, Beijing, China.
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, 100084, Beijing, China.
| | - Lu Fang
- Department of Electronic Engineering, Tsinghua University, 100084, Beijing, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, 100084, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China.
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, 100084, Beijing, China.
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, 100084, Beijing, China.
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31
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Affiliation(s)
- Xinyang Li
- Department of Automation, Tsinghua University, Beijing, China
| | - Yuanlong Zhang
- Department of Automation, Tsinghua University, Beijing, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
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32
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Feng BY, Guo H, Xie M, Boominathan V, Sharma MK, Veeraraghavan A, Metzler CA. NeuWS: Neural wavefront shaping for guidestar-free imaging through static and dynamic scattering media. SCIENCE ADVANCES 2023; 9:eadg4671. [PMID: 37379386 DOI: 10.1126/sciadv.adg4671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
Diffraction-limited optical imaging through scattering media has the potential to transform many applications such as airborne and space-based imaging (through the atmosphere), bioimaging (through skin and human tissue), and fiber-based imaging (through fiber bundles). Existing wavefront shaping methods can image through scattering media and other obscurants by optically correcting wavefront aberrations using high-resolution spatial light modulators-but these methods generally require (i) guidestars, (ii) controlled illumination, (iii) point scanning, and/or (iv) statics scenes and aberrations. We propose neural wavefront shaping (NeuWS), a scanning-free wavefront shaping technique that integrates maximum likelihood estimation, measurement modulation, and neural signal representations to reconstruct diffraction-limited images through strong static and dynamic scattering media without guidestars, sparse targets, controlled illumination, nor specialized image sensors. We experimentally demonstrate guidestar-free, wide field-of-view, high-resolution, diffraction-limited imaging of extended, nonsparse, and static/dynamic scenes captured through static/dynamic aberrations.
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Affiliation(s)
- Brandon Y Feng
- Department of Computer Science, The University of Maryland, College Park, College Park, MD 20742, USA
| | - Haiyun Guo
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Mingyang Xie
- Department of Computer Science, The University of Maryland, College Park, College Park, MD 20742, USA
| | - Vivek Boominathan
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Manoj K Sharma
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Ashok Veeraraghavan
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Christopher A Metzler
- Department of Computer Science, The University of Maryland, College Park, College Park, MD 20742, USA
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33
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Yun H, Saavedra G, Garcia-Sucerquia J, Tolosa A, Martinez-Corral M, Sanchez-Ortiga E. Practical guide for setting up a Fourier light-field microscope. APPLIED OPTICS 2023; 62:4228-4235. [PMID: 37706910 DOI: 10.1364/ao.491369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/26/2023] [Indexed: 09/15/2023]
Abstract
A practical guide for the easy implementation of a Fourier light-field microscope is reported. The Fourier light-field concept applied to microscopy allows the capture in real time of a series of 2D orthographic images of microscopic thick dynamic samples. Such perspective images contain spatial and angular information of the light-field emitted by the sample. A feature of this technology is the tight requirement of a double optical conjugation relationship, and also the requirement of NA matching. For these reasons, the Fourier light-field microscope being a non-complex optical system, a clear protocol on how to set up the optical elements accurately is needed. In this sense, this guide is aimed to simplify the implementation process, with an optical bench and off-the-shelf components. This will help the widespread use of this recent technology.
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Li B, Zhu L, Li B, Feng W, Lian X, Ji X. Efficient framework of solving time-gated reflection matrix for imaging through turbid medium. OPTICS EXPRESS 2023; 31:15461-15473. [PMID: 37157647 DOI: 10.1364/oe.488257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Imaging through turbid medium is a long pursuit in many research fields, such as biomedicine, astronomy and automatic vehicle, in which the reflection matrix-based method is a promising solution. However, the epi-detection geometry suffers from round-trip distortion and it is challenging to isolate the input and output aberrations in non-ideal cases due to system imperfections and measurement noises. Here, we present an efficient framework based on single scattering accumulation together with phase unwrapping that can accurately separate input and output aberrations from the noise-affected reflection matrix. We propose to only correct the output aberration while suppressing the input aberration by incoherent averaging. The proposed method is faster in convergence and more robust against noise, avoiding precise and tedious system adjustments. In both simulations and experiments, we demonstrate the diffraction-limited resolution capability under optical thickness beyond 10 scattering mean free paths, showing the potential of applications in neuroscience and dermatology.
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Zhao Z, Zhou Y, Liu B, He J, Zhao J, Cai Y, Fan J, Li X, Wang Z, Lu Z, Wu J, Qi H, Dai Q. Two-photon synthetic aperture microscopy for minimally invasive fast 3D imaging of native subcellular behaviors in deep tissue. Cell 2023; 186:2475-2491.e22. [PMID: 37178688 DOI: 10.1016/j.cell.2023.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/21/2023] [Accepted: 04/10/2023] [Indexed: 05/15/2023]
Abstract
Holistic understanding of physio-pathological processes requires noninvasive 3D imaging in deep tissue across multiple spatial and temporal scales to link diverse transient subcellular behaviors with long-term physiogenesis. Despite broad applications of two-photon microscopy (TPM), there remains an inevitable tradeoff among spatiotemporal resolution, imaging volumes, and durations due to the point-scanning scheme, accumulated phototoxicity, and optical aberrations. Here, we harnessed the concept of synthetic aperture radar in TPM to achieve aberration-corrected 3D imaging of subcellular dynamics at a millisecond scale for over 100,000 large volumes in deep tissue, with three orders of magnitude reduction in photobleaching. With its advantages, we identified direct intercellular communications through migrasome generation following traumatic brain injury, visualized the formation process of germinal center in the mouse lymph node, and characterized heterogeneous cellular states in the mouse visual cortex, opening up a horizon for intravital imaging to understand the organizations and functions of biological systems at a holistic level.
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Affiliation(s)
- Zhifeng Zhao
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China
| | - Yiliang Zhou
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China
| | - Bo Liu
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Laboratory of Dynamic Immunobiology, Institute for Immunology, Tsinghua University, Beijing 100084, China; Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jing He
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Jiayin Zhao
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518071, China
| | - Yeyi Cai
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Jingtao Fan
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China
| | - Xinyang Li
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China; Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518071, China
| | - Zilin Wang
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Department of Anesthesiology, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhi Lu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
| | - Hai Qi
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Laboratory of Dynamic Immunobiology, Institute for Immunology, Tsinghua University, Beijing 100084, China; Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua University, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
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Lu Z, Liu Y, Jin M, Luo X, Yue H, Wang Z, Zuo S, Zeng Y, Fan J, Pang Y, Wu J, Yang J, Dai Q. Virtual-scanning light-field microscopy for robust snapshot high-resolution volumetric imaging. Nat Methods 2023; 20:735-746. [PMID: 37024654 PMCID: PMC10172145 DOI: 10.1038/s41592-023-01839-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
High-speed three-dimensional (3D) intravital imaging in animals is useful for studying transient subcellular interactions and functions in health and disease. Light-field microscopy (LFM) provides a computational solution for snapshot 3D imaging with low phototoxicity but is restricted by low resolution and reconstruction artifacts induced by optical aberrations, motion and noise. Here, we propose virtual-scanning LFM (VsLFM), a physics-based deep learning framework to increase the resolution of LFM up to the diffraction limit within a snapshot. By constructing a 40 GB high-resolution scanning LFM dataset across different species, we exploit physical priors between phase-correlated angular views to address the frequency aliasing problem. This enables us to bypass hardware scanning and associated motion artifacts. Here, we show that VsLFM achieves ultrafast 3D imaging of diverse processes such as the beating heart in embryonic zebrafish, voltage activity in Drosophila brains and neutrophil migration in the mouse liver at up to 500 volumes per second.
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Affiliation(s)
- Zhi Lu
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Yu Liu
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Manchang Jin
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Xin Luo
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Huanjing Yue
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Zian Wang
- Department of Automation, Tsinghua University, Beijing, China
| | - Siqing Zuo
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Yunmin Zeng
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Jiaqi Fan
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Yanwei Pang
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
| | - Jingyu Yang
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
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Zhang Y, Zhang G, Han X, Wu J, Li Z, Li X, Xiao G, Xie H, Fang L, Dai Q. Rapid detection of neurons in widefield calcium imaging datasets after training with synthetic data. Nat Methods 2023; 20:747-754. [PMID: 37002377 PMCID: PMC10172132 DOI: 10.1038/s41592-023-01838-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/07/2023] [Indexed: 04/03/2023]
Abstract
AbstractWidefield microscopy can provide optical access to multi-millimeter fields of view and thousands of neurons in mammalian brains at video rate. However, tissue scattering and background contamination results in signal deterioration, making the extraction of neuronal activity challenging, laborious and time consuming. Here we present our deep-learning-based widefield neuron finder (DeepWonder), which is trained by simulated functional recordings and effectively works on experimental data to achieve high-fidelity neuronal extraction. Equipped with systematic background contribution priors, DeepWonder conducts neuronal inference with an order-of-magnitude-faster speed and improved accuracy compared with alternative approaches. DeepWonder removes background contaminations and is computationally efficient. Specifically, DeepWonder accomplishes 50-fold signal-to-background ratio enhancement when processing terabytes-scale cortex-wide functional recordings, with over 14,000 neurons extracted in 17 h.
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Wang Y, Zhai WD, Wu C. Algal cell viability assessment: The role of environmental factors in phytoplankton population dynamics. MARINE POLLUTION BULLETIN 2023; 189:114743. [PMID: 36898274 DOI: 10.1016/j.marpolbul.2023.114743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
The viability of algal cells is one of the most fundamental issues in marine ecological research. In this work, a method was designed to identify algal cell viability based on digital holography and deep learning, which divided algal cells into three categories: active, weak, and dead cells. This method was applied to measure algal cells in surface waters of the East China Sea in spring, revealing about 4.34 %-23.29 % weak cells and 3.98 %-19.47 % dead cells. Levels of nitrate and chlorophyll a were the main factors affecting the viability of algal cells. Furthermore, algal viability changes during the heating and cooling were observed in laboratory experiments: high temperatures led to an increase in weak algal cells. This may provide an explanation for why most harmful algal blooms occur in warming months. This study provided a novel insight into how to identify the viability of algal cells and understand their significance in the ocean.
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Affiliation(s)
- Yanyan Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Wei-Dong Zhai
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
| | - Chi Wu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China.
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Zhai J, Jin C, Kong L. Compact, Hybrid Light-Sheet and Fourier Light-Field Microscopy with a Single Objective for High-Speed Volumetric Imaging In Vivo. J Phys Chem A 2023; 127:2873-2879. [PMID: 36926932 DOI: 10.1021/acs.jpca.3c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Volumetric imaging of biodynamics at high spatiotemporal resolutions in vivo is vital in biomedical studies, in which Fourier light field microscopy (FLFM) is a promising technique. However, the commonly used wide-field illumination strategy in FLFM introduces intense out of depth-of-field background, which not only degrades the image quality, but also introduces reconstruction artifacts. Employing light sheet illumination is an effective way to alleviate the background and reduce photobleaching in light-field microscopy. Unfortunately, the introduction of light-sheet illumination often requires an extra objective and precise alignment, which increases the system complexity. Here, we propose the compact, hybrid light-sheet and FLFM (CLS-FLFM), which uses only a single objective to achieve both light-sheet illumination and Fourier light-field imaging simultaneously. With a micromirror under the objective, we focus the light sheet, which ensures selective-volume-illumination, on the imaging plane of the FLFM to perform volumetric imaging. We demonstrate the superior performance of CLS-FLFM in inhibiting background in both structural and dynamical imaging of larval zebrafish in vivo. We envision that CLS-FLFM finds wide applications in high-speed, background-inhibited volumetric imaging of biodynamics in vivo.
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Affiliation(s)
- Jiazhen Zhai
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Cheng Jin
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Lingjie Kong
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China.,IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
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40
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Chen S, Lu Z, Jia H, Yang B, Liu C, Yang Y, Zhang S, Wang Z, Yang L, Li S, Li J, Yang C. Hepatocyte-specific Mas activation enhances lipophagy and fatty acid oxidation to protect against acetaminophen-induced hepatotoxicity in mice. J Hepatol 2023; 78:543-557. [PMID: 36368597 DOI: 10.1016/j.jhep.2022.10.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND & AIMS Acetaminophen (APAP) is the most common cause of drug-induced liver injury (DILI); however, treatment options are limited. Mas is a G protein-coupled receptor whose role in APAP-induced hepatotoxicity has not yet been examined. METHODS Intrahepatic Mas expression was determined in both human and mouse DILI models. Mas1-/-, AlbcreMas1f/f, Ppara-/-, Mas1-/-Ppara-/- and wild-type mice were challenged with APAP for the in vivo analyses of Mas-AKT-FOXO1 axis-dependent lipophagy and fatty acid oxidation (FAO), using pharmacological compounds and genetic tools. Liver samples were collected for RNA-sequencing, proteomics, metabolomics, lipidomics, and metabolic flux analysis. Live-imaging of liver and histological, biochemical, and molecular studies were performed to evaluate APAP-induced hepatotoxicity in mice. Primary hepatocytes and hepatic cell lines were exposed to APAP for in vitro analysis. RESULTS Intrahepatic Mas expression was significantly upregulated in human and mouse DILI models. Mice with systemic, liver-specific, or hepatocyte-specific Mas1 deficiency were vulnerable to APAP-induced hepatotoxicity. They exhibited substantially impaired lipophagy and downstream FAO, which was accompanied by the activation of AKT and suppression of FOXO1. In addition, the prophylactic activation of Mas conferred strong protection against APAP challenge in mice, with remarkably enhanced lipophagy and FAO dependent on the AKT-FOXO1 axis. Moreover, the protective effects of AVE0991 were substantially diminished by the inhibition of either lipophagy or FAO. CONCLUSIONS The activation of Mas on hepatocytes enhanced AKT-FOXO1-dependent lipophagy and downstream FAO, protecting mice from APAP-induced hepatotoxicity and indicating that hepatocyte-specific Mas might be a novel therapeutic target for DILI. IMPACT AND IMPLICATIONS Mas signalling arises as a novel therapeutic target for patients with APAP-induced liver injury. The Mas-AKT/FOXO1-fatty acid degradation pathway could be critical for the development of treatment strategies for APAP overdose. When Mas signalling is targeted, the extent of liver injury should be considered at the time of administration. These findings obtained from APAP-challenged mice still need to be confirmed in a clinical context.
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Affiliation(s)
- Shuai Chen
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Zhi Lu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China
| | - Haoyu Jia
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Bo Yang
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Chun Liu
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yuxin Yang
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shuo Zhang
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Zhijing Wang
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Liu Yang
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Shanshan Li
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jing Li
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China.
| | - Changqing Yang
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China.
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Cui Y, Zhang X, Li X, Lin J. Multiscale microscopy to decipher plant cell structure and dynamics. THE NEW PHYTOLOGIST 2023; 237:1980-1997. [PMID: 36477856 DOI: 10.1111/nph.18641] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
New imaging methodologies with high contrast and molecular specificity allow researchers to analyze dynamic processes in plant cells at multiple scales, from single protein and RNA molecules to organelles and cells, to whole organs and tissues. These techniques produce informative images and quantitative data on molecular dynamics to address questions that cannot be answered by conventional biochemical assays. Here, we review selected microscopy techniques, focusing on their basic principles and applications in plant science, discussing the pros and cons of each technique, and introducing methods for quantitative analysis. This review thus provides guidance for plant scientists in selecting the most appropriate techniques to decipher structures and dynamic processes at different levels, from protein dynamics to morphogenesis.
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Affiliation(s)
- Yaning Cui
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xi Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaojuan Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
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Dong LF, Rohlena J, Zobalova R, Nahacka Z, Rodriguez AM, Berridge MV, Neuzil J. Mitochondria on the move: Horizontal mitochondrial transfer in disease and health. J Cell Biol 2023; 222:213873. [PMID: 36795453 PMCID: PMC9960264 DOI: 10.1083/jcb.202211044] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 02/17/2023] Open
Abstract
Mammalian genes were long thought to be constrained within somatic cells in most cell types. This concept was challenged recently when cellular organelles including mitochondria were shown to move between mammalian cells in culture via cytoplasmic bridges. Recent research in animals indicates transfer of mitochondria in cancer and during lung injury in vivo, with considerable functional consequences. Since these pioneering discoveries, many studies have confirmed horizontal mitochondrial transfer (HMT) in vivo, and its functional characteristics and consequences have been described. Additional support for this phenomenon has come from phylogenetic studies. Apparently, mitochondrial trafficking between cells occurs more frequently than previously thought and contributes to diverse processes including bioenergetic crosstalk and homeostasis, disease treatment and recovery, and development of resistance to cancer therapy. Here we highlight current knowledge of HMT between cells, focusing primarily on in vivo systems, and contend that this process is not only (patho)physiologically relevant, but also can be exploited for the design of novel therapeutic approaches.
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Affiliation(s)
- Lan-Feng Dong
- https://ror.org/02sc3r913School of Pharmacy and Medical Sciences, Griffith University, Southport, Australia,Lan-Feng Dong:
| | - Jakub Rohlena
- https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic
| | - Renata Zobalova
- https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic
| | - Zuzana Nahacka
- https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic
| | | | | | - Jiri Neuzil
- https://ror.org/02sc3r913School of Pharmacy and Medical Sciences, Griffith University, Southport, Australia,https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic,Faculty of Science, Charles University, Prague, Czech Republic,First Faculty of Medicine, Charles University, Prague, Czech Republic,Correspondence to Jiri Neuzil: ,
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Qiu Y, Zhao Z, Yang J, Cheng Y, Liu Y, Yang BR, Qin Z. Light field displays with computational vision correction for astigmatism and high-order aberrations with real-time implementation. OPTICS EXPRESS 2023; 31:6262-6280. [PMID: 36823887 DOI: 10.1364/oe.485547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Vision-correcting near-eye displays are necessary concerning the large population with refractive errors. However, varifocal optics cannot effectively address astigmatism (AST) and high-order aberration (HOAs); freeform optics has little prescription flexibility. Thus, a computational solution is desired to correct AST and HOA with high prescription flexibility and no increase in volume and hardware complexity. In addition, the computational complexity should support real-time rendering. We propose that the light field display can achieve such computational vision correction by manipulating sampling rays so that rays forming a voxel are re-focused on the retina. The ray manipulation merely requires updating the elemental image array (EIA), being a fully computational solution. The correction is first calculated based on an eye's wavefront map and then refined by a simulator performing iterative optimization with a schematic eye model. Using examples of HOA and AST, we demonstrate that corrected EIAs make sampling rays distributed within ±1 arcmin on the retina. Correspondingly, the synthesized image is recovered to nearly as clear as normal vision. We also propose a new voxel-based EIA generation method considering the computational complexity. All voxel positions and the mapping between voxels and their homogeneous pixels are acquired in advance and stored as a lookup table, bringing about an ultra-fast rendering speed of 10 ms per frame with no cost in computing hardware and rendering accuracy. Finally, experimental verification is carried out by introducing the HOA and AST with customized lenses in front of a camera. As a result, significantly recovered images are reported.
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Real-time denoising enables high-sensitivity fluorescence time-lapse imaging beyond the shot-noise limit. Nat Biotechnol 2023; 41:282-292. [PMID: 36163547 PMCID: PMC9931589 DOI: 10.1038/s41587-022-01450-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/29/2022] [Indexed: 11/09/2022]
Abstract
A fundamental challenge in fluorescence microscopy is the photon shot noise arising from the inevitable stochasticity of photon detection. Noise increases measurement uncertainty and limits imaging resolution, speed and sensitivity. To achieve high-sensitivity fluorescence imaging beyond the shot-noise limit, we present DeepCAD-RT, a self-supervised deep learning method for real-time noise suppression. Based on our previous framework DeepCAD, we reduced the number of network parameters by 94%, memory consumption by 27-fold and processing time by a factor of 20, allowing real-time processing on a two-photon microscope. A high imaging signal-to-noise ratio can be acquired with tenfold fewer photons than in standard imaging approaches. We demonstrate the utility of DeepCAD-RT in a series of photon-limited experiments, including in vivo calcium imaging of mice, zebrafish larva and fruit flies, recording of three-dimensional (3D) migration of neutrophils after acute brain injury and imaging of 3D dynamics of cortical ATP release. DeepCAD-RT will facilitate the morphological and functional interrogation of biological dynamics with a minimal photon budget.
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Singh R, Subramanian K, Power RM, Paix A, Gil A, Ikmi A, Prevedel R. Oblique plane microscope for mesoscopic imaging of freely moving organisms with cellular resolution. OPTICS EXPRESS 2023; 31:2292-2301. [PMID: 36785246 DOI: 10.1364/oe.471845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/25/2022] [Indexed: 05/25/2023]
Abstract
Several important questions in biology require non-invasive and three-dimensional imaging techniques with an appropriate spatiotemporal resolution that permits live organisms to move in an unconstrained fashion over an extended field-of-view. While selective-plane illumination microscopy (SPIM) has emerged as a powerful method to observe live biological specimens at high spatio-temporal resolution, typical implementations often necessitate constraining sample mounting or lack the required volumetric speed. Here, we report on an open-top, dual-objective oblique plane microscope (OPM) capable of observing millimeter-sized, freely moving animals at cellular resolution. We demonstrate the capabilities of our mesoscopic OPM (MesOPM) by imaging the behavioral dynamics of the sea anemone Nematostella vectensis over 1.56 × 1.56 × 0.25 mm at 1.5 × 2.8 × 5.3 µm resolution and 0.5 Hz volume rate.
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Su C, Gao Y, Zhou Y, Sun Y, Yan C, Yin H, Xiong B. AutoDeconJ: a GPU-accelerated ImageJ plugin for 3D light-field deconvolution with optimal iteration numbers predicting. Bioinformatics 2022; 39:6849514. [PMID: 36440906 PMCID: PMC9805591 DOI: 10.1093/bioinformatics/btac760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/25/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
MOTIVATION Light-field microscopy (LFM) is a compact solution to high-speed 3D fluorescence imaging. Usually, we need to do 3D deconvolution to the captured raw data. Although there are deep neural network methods that can accelerate the reconstruction process, the model is not universally applicable for all system parameters. Here, we develop AutoDeconJ, a GPU-accelerated ImageJ plugin for 4.4× faster and more accurate deconvolution of LFM data. We further propose an image quality metric for the deconvolution process, aiding in automatically determining the optimal number of iterations with higher reconstruction accuracy and fewer artifacts. RESULTS Our proposed method outperforms state-of-the-art light-field deconvolution methods in reconstruction time and optimal iteration numbers prediction capability. It shows better universality of different light-field point spread function (PSF) parameters than the deep learning method. The fast, accurate and general reconstruction performance for different PSF parameters suggests its potential for mass 3D reconstruction of LFM data. AVAILABILITY AND IMPLEMENTATION The codes, the documentation and example data are available on an open source at: https://github.com/Onetism/AutoDeconJ.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Changqing Su
- School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai 264209, China,National Engineering Laboratory for Video Technology (NELVT), Peking University, Beijing 100871, China
| | - Yuhan Gao
- Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - You Zhou
- School of Electronic Science and Engineering, Nanjing University, Nanjing 210023, China
| | - Yaoqi Sun
- Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - Chenggang Yan
- School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai 264209, China,Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - Haibing Yin
- Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - Bo Xiong
- To whom correspondence should be addressed.
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Feng F, Liang C, Chen D, Du K, Yang R, Lu C, Chen S, Chen L, Tao L, Mao H. Space-variant Shack-Hartmann wavefront sensing based on affine transformation estimation. APPLIED OPTICS 2022; 61:9342-9349. [PMID: 36606880 DOI: 10.1364/ao.471225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/10/2022] [Indexed: 06/17/2023]
Abstract
The space-variant wavefront reconstruction problem inherently exists in deep tissue imaging. In this paper, we propose a framework of Shack-Hartmann wavefront space-variant sensing with extended source illumination. The space-variant wavefront is modeled as a four-dimensional function where two dimensions are in the spatial domain and two are in the Fourier domain with priors that both gently vary. Here, the affine transformation is used to characterize the wavefront space-variant function. Correspondingly, the zonal and modal methods are both escalated to adapt to four-dimensional representation and reconstruction. Experiments and simulations show double to quadruple improvements in space-variant wavefront reconstruction accuracy compared to the conventional space-invariant correlation method.
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Marki A, Ley K. The expanding family of neutrophil-derived extracellular vesicles. Immunol Rev 2022; 312:52-60. [PMID: 35665941 PMCID: PMC10111154 DOI: 10.1111/imr.13103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/15/2022]
Abstract
Neutrophils are immune cells involved in several inflammatory and homeostatic processes. Their capacity to release cargo can be classified based on whether the cargo is released on its own, or in conjunction with plasma membrane structures. Examples of plasma membrane-free secretion modes are degranulation, neutrophil extracellular trap (NET) release, and cytokine release through inflammasome formation. The most studied membrane-covered neutrophil-derived structures are exosomes and ectosomes that are collectively called extracellular vesicles (EV). Apoptotic vesicles are another recognized EV subtype. Over the last decade, additional membrane-covered neutrophil-derived structures were characterized: migratory cytoplasts, migrasomes, and elongated neutrophil-derived structures (ENDS). All these structures are smaller than the neutrophils, cannot reproduce themselves, and thus meet the latest consensus definition of EVs. In this review, we focus on the less well-studied neutrophil EVs: apoptotic vesicles, cytoplasts, migrasomes, and ENDS.
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Affiliation(s)
- Alex Marki
- AstraZeneca, Gaithersburg, Maryland, USA
| | - Klaus Ley
- La Jolla Institute for Immunology and Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA
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Yu S, Yu L. Migrasome biogenesis and functions. FEBS J 2022; 289:7246-7254. [PMID: 34492154 PMCID: PMC9786993 DOI: 10.1111/febs.16183] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 01/13/2023]
Abstract
The migrasome is a newly discovered organelle produced by migrating cells. As cells migrate, long and thin retraction fibers are left in their wake. On these fibers, we discovered the production of a pomegranate-like structure, which we named migrasomes. The production of migrasomes is highly correlated with the migration of cells. Currently, it has been demonstrated the migrasomes exhibit three modes of action: release of signaling molecules through rupturing or leaking, carriers of damaged mitochondria, and lateral transfer of mRNA or proteins. In this review, we would like to discuss, in detail, the functions, mechanisms, and potential applications of this newly discovered cell organelle.
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Affiliation(s)
- Shunbang Yu
- State Key Laboratory of Membrane BiologyBeijing Frontier Research Center for Biological StructureSchool of Life ScienceTsinghua University‐Peking University Joint Center for Life SciencesTsinghua UniversityBeijingChina
| | - Li Yu
- State Key Laboratory of Membrane BiologyBeijing Frontier Research Center for Biological StructureSchool of Life ScienceTsinghua University‐Peking University Joint Center for Life SciencesTsinghua UniversityBeijingChina
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Yoon S, Cheon SY, Park S, Lee D, Lee Y, Han S, Kim M, Koo H. Recent advances in optical imaging through deep tissue: imaging probes and techniques. Biomater Res 2022; 26:57. [PMID: 36273205 PMCID: PMC9587606 DOI: 10.1186/s40824-022-00303-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/22/2022] [Indexed: 12/04/2022] Open
Abstract
Optical imaging has been essential for scientific observations to date, however its biomedical applications has been restricted due to its poor penetration through tissues. In living tissue, signal attenuation and limited imaging depth caused by the wave distortion occur because of scattering and absorption of light by various molecules including hemoglobin, pigments, and water. To overcome this, methodologies have been proposed in the various fields, which can be mainly categorized into two stategies: developing new imaging probes and optical techniques. For example, imaging probes with long wavelength like NIR-II region are advantageous in tissue penetration. Bioluminescence and chemiluminescence can generate light without excitation, minimizing background signals. Afterglow imaging also has high a signal-to-background ratio because excitation light is off during imaging. Methodologies of adaptive optics (AO) and studies of complex media have been established and have produced various techniques such as direct wavefront sensing to rapidly measure and correct the wave distortion and indirect wavefront sensing involving modal and zonal methods to correct complex aberrations. Matrix-based approaches have been used to correct the high-order optical modes by numerical post-processing without any hardware feedback. These newly developed imaging probes and optical techniques enable successful optical imaging through deep tissue. In this review, we discuss recent advances for multi-scale optical imaging within deep tissue, which can provide reseachers multi-disciplinary understanding and broad perspectives in diverse fields including biophotonics for the purpose of translational medicine and convergence science.
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Affiliation(s)
- Seokchan Yoon
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Seo Young Cheon
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Sangjun Park
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Donghyun Lee
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Yeeun Lee
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Seokyoung Han
- Department of Mechanical Engineering, University of Louisville, Louisville, KY, 40208, USA
| | - Moonseok Kim
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
| | - Heebeom Koo
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea. .,Catholic Photomedicine Research Institute, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
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