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Li Y, Zhou Y, Du Y, Gao P, Yang L, Wang W. In vivo Labeling and Intravital Imaging of Bacterial Infection using a Near-infrared Fluorescent D-Amino Acid Probe. Chembiochem 2024; 25:e202400283. [PMID: 38715148 DOI: 10.1002/cbic.202400283] [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: 03/28/2024] [Revised: 04/28/2024] [Indexed: 06/27/2024]
Abstract
Bacterial infections still pose a severe threat to public health, necessitating novel tools for real-time analysis of microbial behaviors in living organisms. While genetically engineered strains with fluorescent or luminescent reporters are commonly used in tracking bacteria, their in vivo uses are often limited. Here, we report a near-infrared fluorescent D-amino acid (FDAA) probe, Cy7ADA, for in situ labeling and intravital imaging of bacterial infections in mice. Cy7ADA probe effectively labels various bacteria in vitro and pathogenic Staphylococcus aureus in mice after intraperitoneal injection. Because of Cy7's high tissue penetration and the quick excretion of free probes via urine, real-time visualization of the pathogens in a liver abscess model via intravital confocal microscopy is achieved. The biodistributions, including their intracellular localization within Kupffer cells, are revealed. Monitoring bacterial responses to antibiotics also demonstrates Cy7ADA's capability to reflect the bacterial load dynamics within the host. Furthermore, Cy7ADA facilitates three-dimensional pathogen imaging in tissue-cleared liver samples, showcasing its potential for studying the biogeography of microbes in different organs. Integrating near-infrared FDAA probes with intravital microscopy holds promise for wide applications in studying bacterial infections in vivo.
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Affiliation(s)
- Yixuan Li
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, China
| | - Yingjun Zhou
- State Key Laboratory of Genetic Engineering, Department of Microbiology, Microbiome Center, School of Life Sciences, Fudan University, Shanghai, China
| | - Yahui Du
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Po Gao
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, China
| | - Liqun Yang
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, China
| | - Wei Wang
- State Key Laboratory of Genetic Engineering, Department of Microbiology, Microbiome Center, School of Life Sciences, Fudan University, Shanghai, China
- Beijing National Laboratory for Molecular Sciences, Beijing, China
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2
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Gauberg J, Moreno KB, Jayaraman K, Abumeri S, Jenkins S, Salazar AM, Meharena HS, Glasgow SM. Spinal motor neuron development and metabolism are transcriptionally regulated by Nuclear Factor IA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600888. [PMID: 38979382 PMCID: PMC11230388 DOI: 10.1101/2024.06.26.600888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Neural circuits governing all motor behaviors in vertebrates rely on the proper development of motor neurons and their precise targeting of limb muscles. Transcription factors are essential for motor neuron development, regulating their specification, migration, and axonal targeting. While transcriptional regulation of the early stages of motor neuron specification is well-established, much less is known about the role of transcription factors in the later stages of maturation and terminal arborization. Defining the molecular mechanisms of these later stages is critical for elucidating how motor circuits are constructed. Here, we demonstrate that the transcription factor Nuclear Factor-IA (NFIA) is required for motor neuron positioning, axonal branching, and neuromuscular junction formation. Moreover, we find that NFIA is required for proper mitochondrial function and ATP production, providing a new and important link between transcription factors and metabolism during motor neuron development. Together, these findings underscore the critical role of NFIA in instructing the assembly of spinal circuits for movement.
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Chen Y, Yang H, Luo Y, Niu Y, Yu M, Deng S, Wang X, Deng H, Chen H, Gao L, Li X, Xu P, Xue F, Miao J, Shi SH, Zhong Y, Ma C, Lei B. Photoacoustic Tomography with Temporal Encoding Reconstruction (PATTERN) for cross-modal individual analysis of the whole brain. Nat Commun 2024; 15:4228. [PMID: 38762498 PMCID: PMC11102525 DOI: 10.1038/s41467-024-48393-z] [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: 07/08/2023] [Accepted: 04/26/2024] [Indexed: 05/20/2024] Open
Abstract
Cross-modal analysis of the same whole brain is an ideal strategy to uncover brain function and dysfunction. However, it remains challenging due to the slow speed and destructiveness of traditional whole-brain optical imaging techniques. Here we develop a new platform, termed Photoacoustic Tomography with Temporal Encoding Reconstruction (PATTERN), for non-destructive, high-speed, 3D imaging of ex vivo rodent, ferret, and non-human primate brains. Using an optimally designed image acquisition scheme and an accompanying machine-learning algorithm, PATTERN extracts signals of genetically-encoded probes from photobleaching-based temporal modulation and enables reliable visualization of neural projection in the whole central nervous system with 3D isotropic resolution. Without structural and biological perturbation to the sample, PATTERN can be combined with other whole-brain imaging modalities to acquire the whole-brain image with both high resolution and morphological fidelity. Furthermore, cross-modal transcriptome analysis of an individual brain is achieved by PATTERN imaging. Together, PATTERN provides a compatible and versatile strategy for brain-wide cross-modal analysis at the individual level.
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Affiliation(s)
- Yuwen Chen
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, PR China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, 100084, PR China
| | - Haoyu Yang
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
- IDG/McGovern Institute of Brain Research, Beijing, 100084, PR China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Yan Luo
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, PR China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, 100084, PR China
| | - Yijun Niu
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
- IDG/McGovern Institute of Brain Research, Beijing, 100084, PR China
| | - Muzhou Yu
- School of Computer Science, Xi'an Jiaotong University, Xi'an, 713599, PR China
| | - Shanjun Deng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Xuanhao Wang
- Research Center for Humanoid Sensing, Zhejiang Laboratory, Hangzhou, 311100, PR China
| | - Handi Deng
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, PR China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, 100084, PR China
| | - Haichao Chen
- School of Medicine, Tsinghua University, Beijing, 100084, PR China
| | - Lixia Gao
- Department of Neurology of the Second Affiliated Hospital and Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Zhejiang University, Hangzhou, 310029, PR China
| | - Xinjian Li
- Department of Neurology of the Second Affiliated Hospital and Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Zhejiang University, Hangzhou, 310029, PR China
| | - Pingyong Xu
- Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Fudong Xue
- Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Jing Miao
- Canterbury School, New Milford, CT, 06776, USA
| | - Song-Hai Shi
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
- IDG/McGovern Institute of Brain Research, Beijing, 100084, PR China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Yi Zhong
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
- IDG/McGovern Institute of Brain Research, Beijing, 100084, PR China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Cheng Ma
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, PR China.
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, 100084, PR China.
| | - Bo Lei
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China.
- IDG/McGovern Institute of Brain Research, Beijing, 100084, PR China.
- Beijing Academy of Artificial Intelligence, Beijing, 100084, PR China.
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Reynaud-Dulaurier R, Clément R, Yjjou S, Cresson C, Saoudi Y, Faideau M, Decressac M. The Blood-Brain Barrier Is Unaffected in the Ndufs4-/- Mouse Model of Leigh Syndrome. Int J Mol Sci 2024; 25:4828. [PMID: 38732047 PMCID: PMC11084937 DOI: 10.3390/ijms25094828] [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: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Mitochondrial dysfunction plays a major role in physiological aging and in many pathological conditions. Yet, no study has explored the consequence of primary mitochondrial deficiency on the blood-brain barrier (BBB) structure and function. Addressing this question has major implications for pharmacological and genetic strategies aimed at ameliorating the neurological symptoms that are often predominant in patients suffering from these conditions. In this study, we examined the permeability of the BBB in the Ndufs4-/- mouse model of Leigh syndrome (LS). Our results indicated that the structural and functional integrity of the BBB was preserved in this severe model of mitochondrial disease. Our findings suggests that pharmacological or gene therapy strategies targeting the central nervous system in this mouse model and possibly other models of mitochondrial dysfunction require the use of specific tools to bypass the BBB. In addition, they raise the need for testing the integrity of the BBB in complementary in vivo models.
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Affiliation(s)
| | | | | | | | | | | | - Michael Decressac
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neurosciences, Université Grenoble Alpes, 38000 Grenoble, France; (R.R.-D.); (R.C.); (S.Y.); (C.C.); (Y.S.); (M.F.)
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5
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Gao P, Rivera M, Lin X, Holmes TC, Zhao H, Xu X. Immunolabeling-compatible PEGASOS tissue clearing for high-resolution whole mouse brain imaging. Front Neural Circuits 2024; 18:1345692. [PMID: 38694272 PMCID: PMC11061518 DOI: 10.3389/fncir.2024.1345692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/13/2024] [Indexed: 05/04/2024] Open
Abstract
Novel brain clearing methods revolutionize imaging by increasing visualization throughout the brain at high resolution. However, combining the standard tool of immunostaining targets of interest with clearing methods has lagged behind. We integrate whole-mount immunostaining with PEGASOS tissue clearing, referred to as iPEGASOS (immunostaining-compatible PEGASOS), to address the challenge of signal quenching during clearing processes. iPEGASOS effectively enhances molecular-genetically targeted fluorescent signals that are otherwise compromised during conventional clearing procedures. Additionally, we demonstrate the utility of iPEGASOS for visualizing neurochemical markers or viral labels to augment visualization that transgenic mouse lines cannot provide. Our study encompasses three distinct applications, each showcasing the versatility and efficacy of this approach. We employ whole-mount immunostaining to enhance molecular signals in transgenic reporter mouse lines to visualize the whole-brain spatial distribution of specific cellular populations. We also significantly improve the visualization of neural circuit connections by enhancing signals from viral tracers injected into the brain. Last, we show immunostaining without genetic markers to selectively label beta-amyloid deposits in a mouse model of Alzheimer's disease, facilitating the comprehensive whole-brain study of pathological features.
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Affiliation(s)
- Pan Gao
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Matthew Rivera
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Xiaoxiao Lin
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Todd C. Holmes
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, United States
- Center for Neural Circuit Mapping, University of California, Irvine, Irvine, CA, United States
| | - Hu Zhao
- Chinese Institute for Brain Research, Beijing, China
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
- Center for Neural Circuit Mapping, University of California, Irvine, Irvine, CA, United States
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6
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Mai H, Luo J, Hoeher L, Al-Maskari R, Horvath I, Chen Y, Kofler F, Piraud M, Paetzold JC, Modamio J, Todorov M, Elsner M, Hellal F, Ertürk A. Whole-body cellular mapping in mouse using standard IgG antibodies. Nat Biotechnol 2024; 42:617-627. [PMID: 37430076 PMCID: PMC11021200 DOI: 10.1038/s41587-023-01846-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/26/2023] [Indexed: 07/12/2023]
Abstract
Whole-body imaging techniques play a vital role in exploring the interplay of physiological systems in maintaining health and driving disease. We introduce wildDISCO, a new approach for whole-body immunolabeling, optical clearing and imaging in mice, circumventing the need for transgenic reporter animals or nanobody labeling and so overcoming existing technical limitations. We identified heptakis(2,6-di-O-methyl)-β-cyclodextrin as a potent enhancer of cholesterol extraction and membrane permeabilization, enabling deep, homogeneous penetration of standard antibodies without aggregation. WildDISCO facilitates imaging of peripheral nervous systems, lymphatic vessels and immune cells in whole mice at cellular resolution by labeling diverse endogenous proteins. Additionally, we examined rare proliferating cells and the effects of biological perturbations, as demonstrated in germ-free mice. We applied wildDISCO to map tertiary lymphoid structures in the context of breast cancer, considering both primary tumor and metastases throughout the mouse body. An atlas of high-resolution images showcasing mouse nervous, lymphatic and vascular systems is accessible at http://discotechnologies.org/wildDISCO/atlas/index.php .
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Affiliation(s)
- Hongcheng Mai
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany
- Munich Medical Research School, Munich, Germany
- Deep Piction GmbH, Munich, Germany
| | - Jie Luo
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany
- Deep Piction GmbH, Munich, Germany
| | - Luciano Hoeher
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
| | - Rami Al-Maskari
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Izabela Horvath
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Ying Chen
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany
- Faculty of Medicine, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Florian Kofler
- Helmholtz Al, Helmholtz Center Munich, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Munich, Germany
- TranslaTUM - Central Institute for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Marie Piraud
- Helmholtz Al, Helmholtz Center Munich, Neuherberg, Germany
| | - Johannes C Paetzold
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Department of Computing, Imperial College London, London, UK
| | - Jennifer Modamio
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
| | - Mihail Todorov
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Markus Elsner
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
| | - Farida Hellal
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany.
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany.
- Deep Piction GmbH, Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
- Graduate School of Neuroscience (GSN), Munich, Germany.
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7
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Jin BH, Woo J, Lee M, Ku S, Moon HS, Ryu SJ, Hyun YM, Park JY, Kuh SU, Cho YE. Optimization of the optical transparency of bones by PACT-based passive tissue clearing. Exp Mol Med 2023; 55:2190-2204. [PMID: 37779150 PMCID: PMC10618275 DOI: 10.1038/s12276-023-01089-8] [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: 11/04/2022] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 10/03/2023] Open
Abstract
Recent developments in tissue clearing methods such as the passive clearing technique (PACT) have allowed three-dimensional analysis of biological structures in whole, intact tissues, thereby providing a greater understanding of spatial relationships and biological circuits. Nonetheless, the issues that remain in maintaining structural integrity and preventing tissue expansion/shrinkage with rapid clearing still inhibit the wide application of these techniques in hard bone tissues, such as femurs and tibias. Here, we present an optimized PACT-based bone-clearing method, Bone-mPACT+, that protects biological structures. Bone-mPACT+ and four different decalcifying procedures were tested for their ability to improve bone tissue clearing efficiency without sacrificing optical transparency; they rendered nearly all types of bone tissues transparent. Both mouse and rat bones were nearly transparent after the clearing process. We also present a further modification, the Bone-mPACT+ Advance protocol, which is specifically optimized for processing the largest and hardest rat bones for easy clearing and imaging using established tissue clearing methods.
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Affiliation(s)
- Byung-Ho Jin
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
- College of Medicine, Yonsei University Graduate School, Seoul, 03722, Republic of Korea
- Department of Neurosurgery, International ST Mary´s Hospital, College of Medicine, Catholic Kwandong University, Incheon, 22711, Republic of Korea
| | - Jiwon Woo
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Biomedical Research Institute, Biohedron, Seoul, 06230, Republic of Korea
- Biomedical Research Center, Gangnam Severance Hospital, Seoul, 06230, Republic of Korea
| | - Mirae Lee
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Biomedical Research Center, Gangnam Severance Hospital, Seoul, 06230, Republic of Korea
| | - Seockmo Ku
- Department of Food Science and Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Hyung Seok Moon
- Biomedical Research Center, Gangnam Severance Hospital, Seoul, 06230, Republic of Korea
| | - Seung Jun Ryu
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
- Department of Neurosurgery, Daejeon Eulji Medical Center, Eulji University, Daejeon, 35233, Republic of Korea
| | - Young-Min Hyun
- Department of Anatomy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jeong-Yoon Park
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
- College of Medicine, Yonsei University Graduate School, Seoul, 03722, Republic of Korea
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sung Uk Kuh
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
- College of Medicine, Yonsei University Graduate School, Seoul, 03722, Republic of Korea
- Biomedical Research Center, Gangnam Severance Hospital, Seoul, 06230, Republic of Korea
- Department of Medical Device Engineering and Management, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Yong Eun Cho
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea.
- College of Medicine, Yonsei University Graduate School, Seoul, 03722, Republic of Korea.
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
- Department of Neurosurgery, Wiltse Memorial Hospital, Suwon-si, Gyeonggi-do, 16480, Republic of Korea.
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8
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Yip KYT, Gräff J. Tissue clearing applications in memory engram research. Front Behav Neurosci 2023; 17:1181818. [PMID: 37700912 PMCID: PMC10493294 DOI: 10.3389/fnbeh.2023.1181818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/26/2023] [Indexed: 09/14/2023] Open
Abstract
A memory engram is thought to be the physical substrate of the memory trace within the brain, which is generally depicted as a neuronal ensemble activated by learning to fire together during encoding and retrieval. It has been postulated that engram cell ensembles are functionally interconnected across multiple brain regions to store a single memory as an "engram complex", but visualizing this engram complex across the whole brain has for long been hindered by technical limitations. With the recent development of tissue clearing techniques, advanced light-sheet microscopy, and automated 3D image analysis, it has now become possible to generate a brain-wide map of engram cells and thereby to visualize the "engram complex". In this review, we first provide a comprehensive summary of brain-wide engram mapping studies to date. We then compile a guide on implementing the optimal tissue clearing technique for engram tagging approaches, paying particular attention to visualize engram reactivation as a critical mnemonic property, for which whole-brain multiplexed immunostaining becomes a challenging prerequisite. Finally, we highlight the potential of tissue clearing to simultaneously shed light on both the circuit connectivity and molecular underpinnings of engram cells in a single snapshot. In doing so, novel brain regions and circuits can be identified for subsequent functional manipulation, thus providing an opportunity to robustly examine the "engram complex" underlying memory storage.
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Affiliation(s)
| | - Johannes Gräff
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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9
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Wu YC, Moon HG, Bindokas VP, Phillips EH, Park GY, Lee SSY. Multiresolution 3D Optical Mapping of Immune Cell Infiltrates in Mouse Asthmatic Lung. Am J Respir Cell Mol Biol 2023; 69:13-21. [PMID: 37017484 PMCID: PMC10324044 DOI: 10.1165/rcmb.2022-0353ma] [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: 09/06/2022] [Accepted: 04/04/2023] [Indexed: 04/06/2023] Open
Abstract
Asthma is a chronic inflammatory airway disease driven by various infiltrating immune cell types into the lung. Optical microscopy has been used to study immune infiltrates in asthmatic lungs. Confocal laser scanning microscopy (CLSM) identifies the phenotypes and locations of individual immune cells in lung tissue sections by employing high-magnification objectives and multiplex immunofluorescence staining. In contrast, light-sheet fluorescence microscopy (LSFM) can visualize the macroscopic and mesoscopic architecture of whole-mount lung tissues in three dimensions (3D) by adopting an optical tissue-clearing method. Despite each microscopy method producing image data with unique resolution from a tissue sample, CLSM and LSFM have not been applied together because of different tissue-preparation procedures. Here, we introduce a new approach combining LSFM and CLSM into a sequential imaging pipeline. We built a new optical tissue clearing workflow in which the immersion clearing agent can be switched from an organic solvent to an aqueous sugar solution for sequential 3D LSFM and CLSM of mouse lungs. This sequential combination microscopy offered quantitative 3D spatial analyses of the distribution of immune infiltrates in the same mouse asthmatic lung tissue at the organ, tissue, and cell levels. These results show that our method facilitates multiresolution 3D fluorescence microscopy as a new imaging approach providing comprehensive spatial information for a better understanding of inflammatory lung diseases.
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Affiliation(s)
| | - Hyung-Geun Moon
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois
| | - Vytautas P. Bindokas
- Integrated Light Microscopy Facility, The University of Chicago, Chicago, Illinois; and
| | | | - Gye Young Park
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
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10
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Hsu CW, Cerda J, Kirk JM, Turner WD, Rasmussen TL, Flores Suarez CP, Dickinson ME, Wythe JD. EZ Clear for simple, rapid, and robust mouse whole organ clearing. eLife 2022; 11:e77419. [PMID: 36218247 PMCID: PMC9555867 DOI: 10.7554/elife.77419] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Tissue clearing for whole organ cell profiling has revolutionized biology and imaging for exploration of organs in three-dimensional space without compromising tissue architecture. But complicated, laborious procedures, or expensive equipment, as well as the use of hazardous, organic solvents prevent the widespread adoption of these methods. Here, we report a simple and rapid tissue clearing method, EZ Clear, that can clear whole adult mouse organs in 48 hr in just three simple steps. Samples stay at room temperature and remain hydrated throughout the clearing process, preserving endogenous and synthetic fluorescence, without altering sample size. After wholemount clearing and imaging, samples processed with EZ Clear can be subjected to downstream applications, such as tissue embedding and cryosectioning followed by standard histology or immunofluorescent staining without loss of fluorescence signal from endogenous or synthetic reporters. Furthermore, we demonstrate that wholemount adult mouse brains processed with EZ Clear can be successfully immunolabeled for fluorescent imaging while still retaining signal from endogenous fluorescent reporters. Overall, the simplicity, speed, and flexibility of EZ Clear make it easy to adapt and implement in diverse imaging modalities in biomedical research.
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Affiliation(s)
- Chih-Wei Hsu
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
- Optical Imaging and Vital Microscopy Core, Advance Technology Cores, Baylor College of MedicineHoustonUnited States
- Department of Education, Innovation and Technology, Baylor College of MedicineHoustonUnited States
- Cardiovascular Research Institute, Baylor College of MedicineHoustonUnited States
| | - Juan Cerda
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
| | - Jason M Kirk
- Optical Imaging and Vital Microscopy Core, Advance Technology Cores, Baylor College of MedicineHoustonUnited States
| | - Williamson D Turner
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
| | - Tara L Rasmussen
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
- Cardiovascular Research Institute, Baylor College of MedicineHoustonUnited States
| | | | - Mary E Dickinson
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
- Optical Imaging and Vital Microscopy Core, Advance Technology Cores, Baylor College of MedicineHoustonUnited States
- Cardiovascular Research Institute, Baylor College of MedicineHoustonUnited States
| | - Joshua D Wythe
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
- Cardiovascular Research Institute, Baylor College of MedicineHoustonUnited States
- Department of Neurosurgery, Baylor College of MedicineHoustonUnited States
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