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He C, Yuan Y, Gong C, Wang X, Lyu G. Applications of Tissue Clearing in Central and Peripheral Nerves. Neuroscience 2024; 546:104-117. [PMID: 38570062 DOI: 10.1016/j.neuroscience.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
The techniques of tissue clearing have been proposed and applied in anatomical and biomedical research since the 19th century. As we all know, the original study of the nervous system relied on serial ultrathin sections and stereoscopic techniques. The 3D visualization of the nervous system was established by software splicing and reconstruction. With the development of science and technology, microscope equipment had constantly been upgraded. Despite the great progress that has been made in this field, the workload is too complex, and it needs high technical requirements. Abundant mistakes due to manual sections were inescapable and structural integrity remained questionable. According to the classification of tissue transparency methods, we introduced the latest application of transparency methods in central and peripheral nerve research from optical imaging, molecular markers and data analysis. This review summarizes the application of transparent technology in neural pathways. We hope to provide some inspiration for the continuous optimization of tissue clearing methods.
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Affiliation(s)
- Cheng He
- Department of Anatomy, Medical School of Nantong University, Nantong, China
| | - Ye Yuan
- Department of Anatomy, Medical School of Nantong University, Nantong, China
| | - Chuanhui Gong
- Department of Anatomy, Medical School of Nantong University, Nantong, China
| | - Xueying Wang
- Medical School of Nantong University, Nantong, China
| | - Guangming Lyu
- Department of Anatomy, Medical School of Nantong University, Nantong, China; Department of Anatomy, Institute of Neurobiology, Jiangsu Key Laboratory of Neuroregeneration, Medical School of Nantong University, Nantong, China.
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2
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Bao S, Romero JM, Belfort BD, Arenkiel BR. Signaling mechanisms underlying activity-dependent integration of adult-born neurons in the mouse olfactory bulb. Genesis 2024; 62:e23595. [PMID: 38553878 PMCID: PMC10987073 DOI: 10.1002/dvg.23595] [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: 01/10/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/02/2024]
Abstract
Adult neurogenesis has fascinated the field of neuroscience for decades given the prospects of harnessing mechanisms that facilitate the rewiring and/or replacement of adult brain tissue. The subgranular zone of the hippocampus and the subventricular zone of the lateral ventricle are the two main areas in the brain that exhibit ongoing neurogenesis. Of these, adult-born neurons within the olfactory bulb have proven to be a powerful model for studying circuit plasticity, providing a broad and accessible avenue into neuron development, migration, and continued circuit integration within adult brain tissue. This review focuses on some of the recognized molecular and signaling mechanisms underlying activity-dependent adult-born neuron development. Notably, olfactory activity and behavioral states contribute to adult-born neuron plasticity through sensory and centrifugal inputs, in which calcium-dependent transcriptional programs, local translation, and neuropeptide signaling play important roles. This review also highlights areas of needed continued investigation to better understand the remarkable phenomenon of adult-born neuron integration.
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Affiliation(s)
- Suyang Bao
- Development, Disease Models, and Therapeutics Graduate Program, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
| | - Juan M. Romero
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin D.W. Belfort
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
- Genetics and Genomics Graduate Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin R. Arenkiel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
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3
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Soumier A, Lio G, Demily C. Current and future applications of light-sheet imaging for identifying molecular and developmental processes in autism spectrum disorders. Mol Psychiatry 2024:10.1038/s41380-024-02487-8. [PMID: 38443634 DOI: 10.1038/s41380-024-02487-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Autism spectrum disorder (ASD) is identified by a set of neurodevelopmental divergences that typically affect the social communication domain. ASD is also characterized by heterogeneous cognitive impairments and is associated with cooccurring physical and medical conditions. As behaviors emerge as the brain matures, it is particularly essential to identify any gaps in neurodevelopmental trajectories during early perinatal life. Here, we introduce the potential of light-sheet imaging for studying developmental biology and cross-scale interactions among genetic, cellular, molecular and macroscale levels of circuitry and connectivity. We first report the core principles of light-sheet imaging and the recent progress in studying brain development in preclinical animal models and human organoids. We also present studies using light-sheet imaging to understand the development and function of other organs, such as the skin and gastrointestinal tract. We also provide information on the potential of light-sheet imaging in preclinical drug development. Finally, we speculate on the translational benefits of light-sheet imaging for studying individual brain-body interactions in advancing ASD research and creating personalized interventions.
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Affiliation(s)
- Amelie Soumier
- Le Vinatier Hospital Center, 95 boulevard Pinel, 69675, Bron cedex, France.
- iMIND, Center of Excellence for Autism, 95 boulevard Pinel, 69675, Bron cedex, France.
- Institute of Cognitive Science Marc Jeannerod, CNRS, UMR 5229, 67 boulevard Pinel, 69675, Bron cedex, France.
- University Claude Bernard Lyon 1, 43 boulevard du 11 Novembre 1918, 69622, Villeurbanne cedex, France.
| | - Guillaume Lio
- Le Vinatier Hospital Center, 95 boulevard Pinel, 69675, Bron cedex, France
- iMIND, Center of Excellence for Autism, 95 boulevard Pinel, 69675, Bron cedex, France
- Institute of Cognitive Science Marc Jeannerod, CNRS, UMR 5229, 67 boulevard Pinel, 69675, Bron cedex, France
| | - Caroline Demily
- Le Vinatier Hospital Center, 95 boulevard Pinel, 69675, Bron cedex, France
- iMIND, Center of Excellence for Autism, 95 boulevard Pinel, 69675, Bron cedex, France
- Institute of Cognitive Science Marc Jeannerod, CNRS, UMR 5229, 67 boulevard Pinel, 69675, Bron cedex, France
- University Claude Bernard Lyon 1, 43 boulevard du 11 Novembre 1918, 69622, Villeurbanne cedex, France
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4
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Ushakov DS, Finke S. Tissue optical clearing and 3D imaging of virus infections. Adv Virus Res 2023; 116:89-121. [PMID: 37524483 DOI: 10.1016/bs.aivir.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Imaging pathogens within 3D environment of biological tissues provides spatial information about their localization and interactions with the host. Technological advances in fluorescence microscopy and 3D image analysis now permit visualization and quantification of pathogens directly in large tissue volumes and in great detail. In recent years large volume imaging became an important tool in virology research helping to understand the properties of viruses and the host response to infection. In this chapter we give a review of fluorescence microscopy modalities and tissue optical clearing methods used for large volume tissue imaging. A summary of recent applications for virus research is provided with particular emphasis on studies using light sheet fluorescence microscopy. We describe the challenges and approaches for volumetric image analysis. Practical examples of volumetric imaging implemented in virology laboratories and addressing specialized research questions, such as virus tropism and immune host response are described. We conclude with an overview of the emerging technologies and their potential for virus research.
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Affiliation(s)
- Dmitry S Ushakov
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
| | - Stefan Finke
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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5
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Battistella E, Quintana JF, McConnell G. Application of Light-Sheet Mesoscopy to Image Host-Pathogen Interactions in Intact Organs. Front Cell Infect Microbiol 2022; 12:903957. [PMID: 35774409 PMCID: PMC9237429 DOI: 10.3389/fcimb.2022.903957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/17/2022] [Indexed: 11/17/2022] Open
Abstract
Human African Trypanosomiasis (HAT) is a disease caused by the extracellular parasite Trypanosoma brucei that affects the central nervous system (CNS) during the chronic stage of the infection, inducing neuroinflammation, coma, and death if left untreated. However, little is known about the structural change happening in the brain as result of the infection. So far, infection-induced neuroinflammation has been observed with conventional methods, such as immunohistochemistry, electron microscopy, and 2-photon microscopy only in small portions of the brain, which may not be representative of the disease. In this paper, we have used a newly-developed light-sheet illuminator to image the level of neuroinflammation in chronically infected mice and compared it to naïve controls. This system was developed for imaging in combination with the Mesolens objective lens, providing fast sub-cellular resolution for tens of mm3-large imaging volumes. The mouse brain specimens were cleared using CUBIC+, followed by antibody staining to locate Glial Fibrillary Acid Protein (GFAP) expressing cells, primarily astrocytes and ependymocytes, used here as a proxy for cell reactivity and gliosis. The large capture volume allowed us to detect GFAP+ cells and spatially resolve the response to T. brucei infection. Based on morphometric analyses and spatial distribution of GFAP+ cells, our data demonstrates a significant increase in cell dendrite branching around the lateral ventricle, as well as dorsal and ventral third ventricles, that are negatively correlated with the branch extension in distal sites from the circumventricular spaces. To our knowledge, this is the first report highlighting the potential of light-sheet mesoscopy to characterise the inflammatory responses of the mouse brain to parasitic infection at the cellular level in intact cleared organs, opening new avenues for the development of new mesoscale imaging techniques for the study of host-pathogen interactions.
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Affiliation(s)
- Eliana Battistella
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
- *Correspondence: Eliana Battistella,
| | - Juan F. Quintana
- Wellcome Centre for Integrative Parasitology (WCIP) University of Glasgow, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health, and Comparative Medicine (IBAHCM). University of Glasgow, Glasgow, United Kingdom
| | - Gail McConnell
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
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6
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Qu L, Li Y, Xie P, Liu L, Wang Y, Wu J, Liu Y, Wang T, Li L, Guo K, Wan W, Ouyang L, Xiong F, Kolstad AC, Wu Z, Xu F, Zheng Y, Gong H, Luo Q, Bi G, Dong H, Hawrylycz M, Zeng H, Peng H. Cross-modal coherent registration of whole mouse brains. Nat Methods 2022; 19:111-118. [PMID: 34887551 DOI: 10.1038/s41592-021-01334-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023]
Abstract
Recent whole-brain mapping projects are collecting large-scale three-dimensional images using modalities such as serial two-photon tomography, fluorescence micro-optical sectioning tomography, light-sheet fluorescence microscopy, volumetric imaging with synchronous on-the-fly scan and readout or magnetic resonance imaging. Registration of these multi-dimensional whole-brain images onto a standard atlas is essential for characterizing neuron types and constructing brain wiring diagrams. However, cross-modal image registration is challenging due to intrinsic variations of brain anatomy and artifacts resulting from different sample preparation methods and imaging modalities. We introduce a cross-modal registration method, mBrainAligner, which uses coherent landmark mapping and deep neural networks to align whole mouse brain images to the standard Allen Common Coordinate Framework atlas. We build a brain atlas for the fluorescence micro-optical sectioning tomography modality to facilitate single-cell mapping, and used our method to generate a whole-brain map of three-dimensional single-neuron morphology and neuron cell types.
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Affiliation(s)
- Lei Qu
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Yuanyuan Li
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Peng Xie
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Lijuan Liu
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Ministry of Education Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Yimin Wang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- School of Computer Engineering and Science, Shanghai University, Shanghai, China
| | - Jun Wu
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Yu Liu
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Tao Wang
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Longfei Li
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Kaixuan Guo
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Wan Wan
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Lei Ouyang
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Feng Xiong
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Anna C Kolstad
- Department of Cell, Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhuhao Wu
- Department of Cell, Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fang Xu
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
| | | | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Science, Shanghai, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Science, Shanghai, China
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Guoqiang Bi
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Hongwei Dong
- Center for Integrative Connectomics, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hanchuan Peng
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China.
- Allen Institute for Brain Science, Seattle, WA, USA.
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7
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Schwarz MK, Kubitscheck U. Expansion light sheet fluorescence microscopy of extended biological samples: Applications and perspectives. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 168:33-36. [PMID: 34626664 DOI: 10.1016/j.pbiomolbio.2021.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/25/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Martin K Schwarz
- Institute Experimental Epileptology and Cognition Research (EECR), University of Bonn Medical School, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
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8
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Olfactory Optogenetics: Light Illuminates the Chemical Sensing Mechanisms of Biological Olfactory Systems. BIOSENSORS-BASEL 2021; 11:bios11090309. [PMID: 34562900 PMCID: PMC8470751 DOI: 10.3390/bios11090309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/17/2021] [Accepted: 08/27/2021] [Indexed: 01/26/2023]
Abstract
The mammalian olfactory system has an amazing ability to distinguish thousands of odorant molecules at the trace level. Scientists have made great achievements on revealing the olfactory sensing mechanisms in decades; even though many issues need addressing. Optogenetics provides a novel technical approach to solve this dilemma by utilizing light to illuminate specific part of the olfactory system; which can be used in all corners of the olfactory system for revealing the olfactory mechanism. This article reviews the most recent advances in olfactory optogenetics devoted to elucidate the mechanisms of chemical sensing. It thus attempts to introduce olfactory optogenetics according to the structure of the olfactory system. It mainly includes the following aspects: the sensory input from the olfactory epithelium to the olfactory bulb; the influences of the olfactory bulb (OB) neuron activity patterns on olfactory perception; the regulation between the olfactory cortex and the olfactory bulb; and the neuromodulation participating in odor coding by dominating the olfactory bulb. Finally; current challenges and future development trends of olfactory optogenetics are proposed and discussed.
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9
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Zeppilli S, Ackels T, Attey R, Klimpert N, Ritola KD, Boeing S, Crombach A, Schaefer AT, Fleischmann A. Molecular characterization of projection neuron subtypes in the mouse olfactory bulb. eLife 2021; 10:e65445. [PMID: 34292150 PMCID: PMC8352594 DOI: 10.7554/elife.65445] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
Projection neurons (PNs) in the mammalian olfactory bulb (OB) receive input from the nose and project to diverse cortical and subcortical areas. Morphological and physiological studies have highlighted functional heterogeneity, yet no molecular markers have been described that delineate PN subtypes. Here, we used viral injections into olfactory cortex and fluorescent nucleus sorting to enrich PNs for high-throughput single nucleus and bulk RNA deep sequencing. Transcriptome analysis and RNA in situ hybridization identified distinct mitral and tufted cell populations with characteristic transcription factor network topology, cell adhesion, and excitability-related gene expression. Finally, we describe a new computational approach for integrating bulk and snRNA-seq data and provide evidence that different mitral cell populations preferentially project to different target regions. Together, we have identified potential molecular and gene regulatory mechanisms underlying PN diversity and provide new molecular entry points into studying the diverse functional roles of mitral and tufted cell subtypes.
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Affiliation(s)
- Sara Zeppilli
- Department of Neuroscience, Division of Biology and Medicine, and the Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, and CNRS UMR 7241 and INSERM U1050ParisFrance
| | - Tobias Ackels
- The Francis Crick Institute, Sensory Circuits and Neurotechnology LaboratoryLondonUnited Kingdom
- Department of Neuroscience, Physiology & Pharmacology, University College LondonLondonUnited Kingdom
| | - Robin Attey
- Department of Neuroscience, Division of Biology and Medicine, and the Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Nell Klimpert
- Department of Neuroscience, Division of Biology and Medicine, and the Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Kimberly D Ritola
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Stefan Boeing
- The Francis Crick Institute, Bioinformatics and BiostatisticsLondonUnited Kingdom
- The Francis Crick Institute, Scientific Computing - Digital Development TeamLondonUnited Kingdom
| | - Anton Crombach
- Inria Antenne Lyon La DouaVilleurbanneFrance
- Université de Lyon, INSA-Lyon, LIRIS, UMR 5205VilleurbanneFrance
| | - Andreas T Schaefer
- The Francis Crick Institute, Sensory Circuits and Neurotechnology LaboratoryLondonUnited Kingdom
- Department of Neuroscience, Physiology & Pharmacology, University College LondonLondonUnited Kingdom
| | - Alexander Fleischmann
- Department of Neuroscience, Division of Biology and Medicine, and the Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, and CNRS UMR 7241 and INSERM U1050ParisFrance
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10
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Li Y, Li A, Li J, Zhou H, Cao T, Wang H, Wang K. webTDat: A Web-Based, Real-Time, 3D Visualization Framework for Mesoscopic Whole-Brain Images. Front Neuroinform 2021; 14:542169. [PMID: 33519408 PMCID: PMC7838507 DOI: 10.3389/fninf.2020.542169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Abstract
The popularity of mesoscopic whole-brain imaging techniques has increased dramatically, but these techniques generate teravoxel-sized volumetric image data. Visualizing or interacting with these massive data is both necessary and essential in the bioimage analysis pipeline; however, due to their size, researchers have difficulty using typical computers to process them. The existing solutions do not consider applying web visualization and three-dimensional (3D) volume rendering methods simultaneously to reduce the number of data copy operations and provide a better way to visualize 3D structures in bioimage data. Here, we propose webTDat, an open-source, web-based, real-time 3D visualization framework for mesoscopic-scale whole-brain imaging datasets. webTDat uses an advanced rendering visualization method designed with an innovative data storage format and parallel rendering algorithms. webTDat loads the primary information in the image first and then decides whether it needs to load the secondary information in the image. By performing validation on TB-scale whole-brain datasets, webTDat achieves real-time performance during web visualization. The webTDat framework also provides a rich interface for annotation, making it a useful tool for visualizing mesoscopic whole-brain imaging data.
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Affiliation(s)
- Yuxin Li
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
| | - Anan Li
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China.,HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Junhuai Li
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
| | - Hongfang Zhou
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
| | - Ting Cao
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
| | - Huaijun Wang
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
| | - Kan Wang
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
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11
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Zhao J, Lai HM, Qi Y, He D, Sun H. Current Status of Tissue Clearing and the Path Forward in Neuroscience. ACS Chem Neurosci 2021; 12:5-29. [PMID: 33326739 DOI: 10.1021/acschemneuro.0c00563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Due to the complexity and limited availability of human brain tissues, for decades, pathologists have sought to maximize information gained from individual samples, based on which (patho)physiological processes could be inferred. Recently, new understandings of chemical and physical properties of biological tissues and multiple chemical profiling have given rise to the development of scalable tissue clearing methods allowing superior optical clearing of across-the-scale samples. In the past decade, tissue clearing techniques, molecular labeling methods, advanced laser scanning microscopes, and data visualization and analysis have become commonplace. Combined, they have made 3D visualization of brain tissues with unprecedented resolution and depth widely accessible. To facilitate further advancements and applications, here we provide a critical appraisal of these techniques. We propose a classification system of current tissue clearing and expansion methods that allows users to judge the applicability of individual ones to their questions, followed by a review of the current progress in molecular labeling, optical imaging, and data processing to demonstrate the whole 3D imaging pipeline based on tissue clearing and downstream techniques for visualizing the brain. We also raise the path forward of tissue-clearing-based imaging technology, that is, integrating with state-of-the-art techniques, such as multiplexing protein imaging, in situ signal amplification, RNA detection and sequencing, super-resolution imaging techniques, multiomics studies, and deep learning, for drawing the complete atlas of the human brain and building a 3D pathology platform for central nervous system disorders.
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Affiliation(s)
- Jiajia Zhao
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Hei Ming Lai
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Yuwei Qi
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Dian He
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Haitao Sun
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Clinical Biobank Center, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
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12
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Tsuboi A. LRR-Containing Oncofetal Trophoblast Glycoprotein 5T4 Shapes Neural Circuits in Olfactory and Visual Systems. Front Mol Neurosci 2020; 13:581018. [PMID: 33192298 PMCID: PMC7655536 DOI: 10.3389/fnmol.2020.581018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/22/2020] [Indexed: 01/19/2023] Open
Abstract
In mammals, the sensory experience can regulate the development of various brain structures, including the cortex, hippocampus, retina, and olfactory bulb (OB). Odor experience-evoked neural activity drives the development of dendrites on excitatory projection neurons in the OB, such as mitral and tufted cells, as well as inhibitory interneurons. OB interneurons are generated continuously in the subventricular zone and differentiate into granule cells (GCs) and periglomerular cells (PGCs). However, it remains unknown what role each type of OB interneuron plays in controlling olfactory behaviors. Recent studies showed that among the various types of OB interneurons, a subtype of GCs expressing oncofetal trophoblast glycoprotein 5T4 is required for simple odor detection and discrimination behaviors. Mouse 5T4 (also known as Tpbg) is a type I membrane glycoprotein whose extracellular domain contains seven leucine-rich repeats (LRRs) sandwiched between characteristic LRR-N and LRR-C regions. Recently, it was found that the developmental expression of 5T4 increases dramatically in the retina just before eye-opening. Single-cell transcriptomics further suggests that 5T4 is involved in the development and maintenance of functional synapses in a subset of retinal interneurons, including rod bipolar cells (RBCs) and amacrine cells (ACs). Collectively, 5T4, expressed in interneurons of the OB and retina, plays a key role in sensory processing in the olfactory and visual systems.
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Affiliation(s)
- Akio Tsuboi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
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13
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Ansorge J, Humanes‐Valera D, Pauzin FP, Schwarz MK, Krieger P. Cortical layer 6 control of sensory responses in higher‐order thalamus. J Physiol 2020; 598:3973-4001. [DOI: 10.1113/jp279915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/22/2020] [Indexed: 12/29/2022] Open
Affiliation(s)
- Josephine Ansorge
- Faculty of Medicine, Department of Systems Neuroscience Ruhr University Bochum Bochum Germany
| | - Desire Humanes‐Valera
- Faculty of Medicine, Department of Systems Neuroscience Ruhr University Bochum Bochum Germany
| | - François P. Pauzin
- Faculty of Medicine, Department of Systems Neuroscience Ruhr University Bochum Bochum Germany
| | - Martin K. Schwarz
- Institute of Experimental Epileptology and Cognition Research University of Bonn Medical School Bonn Germany
| | - Patrik Krieger
- Faculty of Medicine, Department of Systems Neuroscience Ruhr University Bochum Bochum Germany
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14
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Ueda HR, Ertürk A, Chung K, Gradinaru V, Chédotal A, Tomancak P, Keller PJ. Tissue clearing and its applications in neuroscience. Nat Rev Neurosci 2020; 21:61-79. [PMID: 31896771 PMCID: PMC8121164 DOI: 10.1038/s41583-019-0250-1] [Citation(s) in RCA: 292] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2019] [Indexed: 02/06/2023]
Abstract
State-of-the-art tissue-clearing methods provide subcellular-level optical access to intact tissues from individual organs and even to some entire mammals. When combined with light-sheet microscopy and automated approaches to image analysis, existing tissue-clearing methods can speed up and may reduce the cost of conventional histology by several orders of magnitude. In addition, tissue-clearing chemistry allows whole-organ antibody labelling, which can be applied even to thick human tissues. By combining the most powerful labelling, clearing, imaging and data-analysis tools, scientists are extracting structural and functional cellular and subcellular information on complex mammalian bodies and large human specimens at an accelerated pace. The rapid generation of terabyte-scale imaging data furthermore creates a high demand for efficient computational approaches that tackle challenges in large-scale data analysis and management. In this Review, we discuss how tissue-clearing methods could provide an unbiased, system-level view of mammalian bodies and human specimens and discuss future opportunities for the use of these methods in human neuroscience.
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Affiliation(s)
- Hiroki R Ueda
- Department of Systems Pharmacology, University of Tokyo, Tokyo, Japan.
- Laboratory for Synthetic Biology, RIKEN BDR, Suita, Japan.
| | - Ali Ertürk
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University of Munich, Munich, Germany
- Institute of Tissue Engineering and Regenerative Medicine, Helmholtz Zentrum München, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Eli & Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for NanoMedicine, Institute for Basic Science, Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering, Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alain Chédotal
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- IT4Innovations, Technical University of Ostrava, Ostrava, Czech Republic
| | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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15
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Schwarz MK, Remy S. Rabies virus-mediated connectivity tracing from single neurons. J Neurosci Methods 2019; 325:108365. [DOI: 10.1016/j.jneumeth.2019.108365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/09/2019] [Accepted: 07/14/2019] [Indexed: 02/01/2023]
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16
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Bohne P, Schwarz MK, Herlitze S, Mark MD. A New Projection From the Deep Cerebellar Nuclei to the Hippocampus via the Ventrolateral and Laterodorsal Thalamus in Mice. Front Neural Circuits 2019; 13:51. [PMID: 31447652 PMCID: PMC6695568 DOI: 10.3389/fncir.2019.00051] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022] Open
Abstract
The cerebellar involvement in cognitive functions such as attention, language, working memory, emotion, goal-directed behavior and spatial navigation is constantly growing. However, an exact connectivity map between the hippocampus and cerebellum in mice is still unknown. Here, we conducted a tracing study to identify the sequence of transsynaptic, cerebellar-hippocampal connections in the mouse brain using combinations of Recombinant adeno-associated virus (rAAV) and pseudotyped deletion-mutant rabies (RABV) viruses. Stereotaxic injection of a primarily anterograde rAAV-WGA (wheat germ agglutinin)-Cre tracer virus in the deep cerebellar nuclei (DCN) of a Cre-dependent tdTomato reporter mouse resulted in strong tdTomato labeling in hippocampal CA1 neurons, retrosplenial cortex (RSC), rhinal cortex (RC) as well as thalamic and cerebellar areas. Whereas hippocampal injections with the retrograde tracer virus rAAV-TTC (tetanus toxin C fragment)-eGFP, displayed eGFP positive cells in the rhinal cortex and subiculum. To determine the sequence of mono-transsynaptic connections between the cerebellum and hippocampus, we used the retrograde tracer RABVΔG-eGFP(EnvA). The tracing revealed a direct connection from the dentate gyrus (DG) in the hippocampus to the RSC, RC and subiculum (S), which are monosynaptically connected to thalamic laterodorsal and ventrolateral areas. These thalamic nuclei are directly connected to cerebellar fastigial (FN), interposed (IntP) and lateral (Lat) nuclei, discovering a new projection route from the fastigial to the laterodorsal thalamic nucleus in the mouse brain. Collectively, our findings suggest a new cerebellar-hippocampal connection via the laterodorsal and ventrolateral thalamus to RSC, RC and S. These results strengthen the notion of the cerebellum's involvement in cognitive functions such as spatial navigation via a polysynaptic circuitry.
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Affiliation(s)
- Pauline Bohne
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
| | - Martin K Schwarz
- Institute of Experimental Epileptology and Cognition Research (EECR), University of Bonn Medical School, Bonn, Germany
| | - Stefan Herlitze
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
| | - Melanie D Mark
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
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17
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Sanz Diez A, Najac M, De Saint Jan D. Basal forebrain GABAergic innervation of olfactory bulb periglomerular interneurons. J Physiol 2019; 597:2547-2563. [PMID: 30920662 DOI: 10.1113/jp277811] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/22/2019] [Indexed: 12/30/2022] Open
Abstract
KEY POINTS Basal forebrain long-range projections to the olfactory bulb are important for olfactory sensitivity and odour discrimination. Using optogenetics, it was confirmed that basal forebrain afferents mediate IPSCs on granule and deep short axon cells. It was also shown that they selectively innervate specific subtypes of periglomerular (PG) cells. Three different subtypes of type 2 PG cells receive GABAergic IPSCs from the basal forebrain but not from other PG cells. Type 1 PG cells, in contrast, do not receive inputs from the basal forebrain but do receive inhibition from other PG cells. These results shed new light on the complexity and specificity of glomerular inhibitory circuits, as well as on their modulation by the basal forebrain. ABSTRACT Olfactory bulb circuits are dominated by multiple inhibitory pathways that finely tune the activity of mitral and tufted cells, the principal neurons, and regulate odour discrimination. Granule cells mediate interglomerular lateral inhibition between mitral and tufted cells' lateral dendrites whereas diverse subtypes of periglomerular (PG) cells mediate intraglomerular lateral inhibition between their apical dendrites. Deep short axon cells form broad intrabulbar inhibitory circuits that regulate both populations of interneurons. Little is known about the extrabulbar GABAergic circuits that control the activity of these various interneurons. We examined this question using patch-clamp recordings and optogenetics in olfactory bulb slices from transgenic mice. We showed that axonal projections emanating from diverse basal forebrain GABAergic neurons densely project in all layers of the olfactory bulb. These long-range GABAergic projections provide a prominent synaptic input on granule and short axon cells in deep layers as well as on selective subtypes of PG cells. Specifically, three different subclasses of type 2 PG cells receive robust and target-specific basal forebrain inputs but have little local interactions with other PG cells. In contrast, type 1 PG cells are not innervated by basal forebrain fibres but do interact with other PG cells. Thus, attention-regulated basal forebrain inputs regulate inhibition in all layers of the olfactory bulb with a previously overlooked synaptic complexity that further defines interneuron subclasses.
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Affiliation(s)
- Alvaro Sanz Diez
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique, Unité Propre de Recherche 3212, Université de Strasbourg, 67084, Strasbourg, France
| | - Marion Najac
- Department of Neurobiology, Northwestern University, Evanston, IL, 60208, USA
| | - Didier De Saint Jan
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique, Unité Propre de Recherche 3212, Université de Strasbourg, 67084, Strasbourg, France
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18
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The Circuit Motif as a Conceptual Tool for Multilevel Neuroscience. Trends Neurosci 2018; 41:128-136. [PMID: 29397990 DOI: 10.1016/j.tins.2018.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 11/07/2017] [Accepted: 01/04/2018] [Indexed: 11/24/2022]
Abstract
Modern neuroscientific techniques that specifically manipulate and measure neuronal activity in behaving animals now allow bridging of the gap from the cellular to the behavioral level. However, in doing so, they also pose new challenges. Research using incompletely defined manipulations in a high-dimensional space without clear hypotheses is likely to suffer from multiple well-known conceptual and statistical problems. In this context it is essential to develop hypotheses with testable implications across levels. Here we propose that a focus on circuit motifs can help achieve this goal. Viewing neural structures as an assembly of circuit motif building blocks is not new. However, recent tool advances have made it possible to extensively map, specifically manipulate, and quantitatively investigate circuit motifs and thereby reexamine their relevance to brain function.
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19
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Yu T, Qi Y, Gong H, Luo Q, Zhu D. Optical clearing for multiscale biological tissues. JOURNAL OF BIOPHOTONICS 2018; 11. [PMID: 29024450 DOI: 10.1002/jbio.201700187] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/08/2017] [Indexed: 05/03/2023]
Abstract
Three-dimensional reconstruction of tissue structures is essential for biomedical research. The development of light microscopes and various fluorescent labeling techniques provides powerful tools for this motivation. However, optical imaging depth suffers from strong light scattering due to inherent heterogeneity of biological tissues. Tissue optical clearing technology provides a distinct solution and permits us to image large volumes with high resolution. Until now, various clearing methods have been developed. In this study, from the perspective of the end users, we review in vitro tissue optical clearing techniques based on the sample features in terms of size and age, enumerate the methods suitable for immunostaining and lipophilic dyes and summarize the combinations with various imaging techniques. We hope this review will be helpful for researchers to choose the most suitable clearing method from a variety of protocols to meet their specific needs.
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Affiliation(s)
- Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MOE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yisong Qi
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MOE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MOE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MOE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MOE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
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20
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Zhang Q, Yang X, Hu Q, Bai K, Yin F, Li N, Gang Y, Wang X, Zeng S. High axial resolution imaging system for large volume tissues using combination of inclined selective plane illumination and mechanical sectioning. BIOMEDICAL OPTICS EXPRESS 2017; 8:5767-5775. [PMID: 29296503 PMCID: PMC5745118 DOI: 10.1364/boe.8.005767] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/06/2017] [Accepted: 09/22/2017] [Indexed: 05/31/2023]
Abstract
To resolve fine structures of biological systems like neurons, it is required to realize microscopic imaging with sufficient spatial resolution in three dimensional systems. With regular optical imaging systems, high lateral resolution is accessible while high axial resolution is hard to achieve in a large volume. We introduce an imaging system for high 3D resolution fluorescence imaging of large volume tissues. Selective plane illumination was adopted to provide high axial resolution. A scientific CMOS working in sub-array mode kept the imaging area in the sample surface, which restrained the adverse effect of aberrations caused by inclined illumination. Plastic embedding and precise mechanical sectioning extended the axial range and eliminated distortion during the whole imaging process. The combination of these techniques enabled 3D high resolution imaging of large tissues. Fluorescent bead imaging showed resolutions of 0.59 μm, 0.47μm, and 0.59 μm in the x, y, and z directions, respectively. Data acquired from the volume sample of brain tissue demonstrated the applicability of this imaging system. Imaging of different depths showed uniform performance where details could be recognized in either the near-soma area or terminal area, and fine structures of neurons could be seen in both the xy and xz sections.
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Affiliation(s)
- Qi Zhang
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiong Yang
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qinglei Hu
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ke Bai
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Fangfang Yin
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ning Li
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yadong Gang
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaojun Wang
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shaoqun Zeng
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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Abstract
Magnetic resonance imaging, positron emission tomography, and optical imaging have emerged as key tools to understand brain function and neurological disorders in preclinical mouse models. They offer the unique advantage of monitoring individual structural and functional changes over time. What remained unsolved until recently was to generate whole-brain microscopy data which can be correlated to the 3D in vivo neuroimaging data. Conventional histological sections are inappropriate especially for neuronal tracing or the unbiased screening for molecular targets through the whole brain. As part of the European Society for Molecular Imaging (ESMI) meeting 2016 in Utrecht, the Netherlands, we addressed this issue in the Molecular Neuroimaging study group meeting. Presentations covered new brain clearing methods, light sheet microscopes for large samples, and automatic registration of microscopy to in vivo imaging data. In this article, we summarize the discussion; give an overview of the novel techniques; and discuss the practical needs, benefits, and limitations.
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22
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Ford NC, Griff ER. Steady-state centrifugal input via the lateral olfactory tract modulates spontaneous activity in the rat main olfactory bulb. Neuroscience 2017; 348:165-179. [PMID: 28215749 DOI: 10.1016/j.neuroscience.2017.02.013] [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: 07/08/2016] [Revised: 01/19/2017] [Accepted: 02/08/2017] [Indexed: 12/01/2022]
Abstract
Mitral and tufted cells in the main olfactory bulb (MOB) of anesthetized rats exhibit vigorous spontaneous activity, action potentials produced in the absence of odor stimuli. The central hypothesis of this paper is that tonic activity of centrifugal input to the MOB modulates the spontaneous activity of MOB neurons. The spontaneous activity of centrifugal fibers causes a baseline of steady-state neurotransmitter release, and odor stimulation produces transient changes in the resulting spontaneous activity. This study evaluated the effect of blocking centrifugal axon conduction in the lateral olfactory tract (LOT) by topically applying 2% lidocaine. Mean spontaneous activity of single bulbar neurons was recorded in each MOB layer before and after lidocaine application. While the spontaneous activity of most MOB neurons reversibly decreased after blockade of the LOT, the spontaneous activity of some neurons in the mitral, tufted and granule cell layers increased. The possible mechanisms producing such changes in spontaneous activity are discussed in terms of the tonic, steady-state release of excitatory and/or inhibitory signals from centrifugal inputs to the MOB. The data show for the first time that tonic centrifugal input to the MOB modulates the spontaneous activity of MOB interneurons and projection neurons. The present study is one of the few that focuses on steady-state spontaneous activity. The modulation of spontaneous activity demonstrated in this study implies a behaviorally relevant, state-dependent regulation of the MOB by the CNS.
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Affiliation(s)
- Neil C Ford
- Department of Biological Sciences, University of Cincinnati, P.O. Box 210006, Cincinnati, OH 45221, USA.
| | - Edwin R Griff
- Department of Biological Sciences, University of Cincinnati, P.O. Box 210006, Cincinnati, OH 45221, USA
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23
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Bohmbach K, Schwarz MK, Schoch S, Henneberger C. The structural and functional evidence for vesicular release from astrocytes in situ. Brain Res Bull 2017; 136:65-75. [PMID: 28122264 DOI: 10.1016/j.brainresbull.2017.01.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/17/2017] [Accepted: 01/19/2017] [Indexed: 12/31/2022]
Abstract
The concept of the tripartite synapse states that bi-directional signalling between perisynaptic astrocyte processes, presynaptic axonal boutons and postsynaptic neuronal structures defines the properties of synaptic information processing. Ca2+-dependent vesicular release from astrocytes, as one of the mechanisms of astrocyte-neuron communication, has attracted particular attention but has also been the subject of intense debate. In neurons, regulated vesicular release is a strongly coordinated process. It requires a complex release machinery comprised of many individual components ranging from vesicular neurotransmitter transporters and soluble NSF attachment protein receptors (SNARE) proteins to Ca2+-sensors and the proteins that spatially and temporally control exocytosis of synaptic vesicles. If astrocytes employ similar mechanisms to release neurotransmitters is less well understood. The aim of this review is therefore to discuss recent experimental evidence that sheds light on the central structural components responsible for vesicular release from astrocytes in situ.
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Affiliation(s)
- Kirsten Bohmbach
- Institute of Cellular Neurosciences, University of Bonn Medical School, Bonn, Germany.
| | - Martin K Schwarz
- Department of Epileptology, University of Bonn Medical School, Bonn, Germany
| | - Susanne Schoch
- Institute of Neuropathology, University of Bonn Medical School, Bonn, Germany
| | - Christian Henneberger
- Institute of Cellular Neurosciences, University of Bonn Medical School, Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; Institute of Neurology, University College London, London, United Kingdom.
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24
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Doerr J, Schwarz MK, Wiedermann D, Leinhaas A, Jakobs A, Schloen F, Schwarz I, Diedenhofen M, Braun NC, Koch P, Peterson DA, Kubitscheck U, Hoehn M, Brüstle O. Whole-brain 3D mapping of human neural transplant innervation. Nat Commun 2017; 8:14162. [PMID: 28102196 PMCID: PMC5253698 DOI: 10.1038/ncomms14162] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 12/05/2016] [Indexed: 11/22/2022] Open
Abstract
While transplantation represents a key tool for assessing in vivo functionality of neural stem cells and their suitability for neural repair, little is known about the integration of grafted neurons into the host brain circuitry. Rabies virus-based retrograde tracing has developed into a powerful approach for visualizing synaptically connected neurons. Here, we combine this technique with light sheet fluorescence microscopy (LSFM) to visualize transplanted cells and connected host neurons in whole-mouse brain preparations. Combined with co-registration of high-precision three-dimensional magnetic resonance imaging (3D MRI) reference data sets, this approach enables precise anatomical allocation of the host input neurons. Our data show that the same neural donor cell population grafted into different brain regions receives highly orthotopic input. These findings indicate that transplant connectivity is largely dictated by the circuitry of the target region and depict rabies-based transsynaptic tracing and LSFM as efficient tools for comprehensive assessment of host–donor cell innervation. Transplantation of cells into the central nervous system has developed into a major avenue for replacing neurons lost to neurodegenerative disease. Here the authors develop an approach combining viral-based transynaptic tracing labeling and whole brain imaging to trace synaptic innervation of human neurons transplanted into a mouse background.
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Affiliation(s)
- Jonas Doerr
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.,Life&Brain GmbH, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Martin Karl Schwarz
- Life&Brain GmbH, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.,Department of Epileptology, Functional Neuroconnectomics Group, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Dirk Wiedermann
- Max Planck Institute for Metabolism Research, In-vivo-NMR Laboratory, Gleuelerstrasse 50, 50931 Cologne, Germany
| | - Anke Leinhaas
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Alina Jakobs
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Florian Schloen
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegeler Strasse 12, 53115 Bonn, Germany
| | - Inna Schwarz
- Department of Epileptology, Functional Neuroconnectomics Group, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Michael Diedenhofen
- Max Planck Institute for Metabolism Research, In-vivo-NMR Laboratory, Gleuelerstrasse 50, 50931 Cologne, Germany
| | - Nils Christian Braun
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Philipp Koch
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Daniel A Peterson
- Center for Stem Cell and Regenerative Medicine, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, 60064 North Chicago, Illinois, USA
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegeler Strasse 12, 53115 Bonn, Germany
| | - Mathias Hoehn
- Max Planck Institute for Metabolism Research, In-vivo-NMR Laboratory, Gleuelerstrasse 50, 50931 Cologne, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.,Life&Brain GmbH, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
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25
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Niedworok CJ, Brown APY, Jorge Cardoso M, Osten P, Ourselin S, Modat M, Margrie TW. aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nat Commun 2016; 7:11879. [PMID: 27384127 PMCID: PMC4941048 DOI: 10.1038/ncomms11879] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/09/2016] [Indexed: 01/16/2023] Open
Abstract
The validation of automated image registration and segmentation is crucial for accurate and reliable mapping of brain connectivity and function in three-dimensional (3D) data sets. While validation standards are necessarily high and routinely met in the clinical arena, they have to date been lacking for high-resolution microscopy data sets obtained from the rodent brain. Here we present a tool for optimized automated mouse atlas propagation (aMAP) based on clinical registration software (NiftyReg) for anatomical segmentation of high-resolution 3D fluorescence images of the adult mouse brain. We empirically evaluate aMAP as a method for registration and subsequent segmentation by validating it against the performance of expert human raters. This study therefore establishes a benchmark standard for mapping the molecular function and cellular connectivity of the rodent brain.
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Affiliation(s)
- Christian J. Niedworok
- The Division of Neurophysiology, MRC National Institute for Medical Research, London NW7 1AA, UK
- The Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK
| | - Alexander P. Y. Brown
- The Division of Neurophysiology, MRC National Institute for Medical Research, London NW7 1AA, UK
- The Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK
| | - M. Jorge Cardoso
- Translational Imaging Group, Centre for Medical Image Computing, University College London, London WC1E 6BT, UK
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sebastien Ourselin
- Translational Imaging Group, Centre for Medical Image Computing, University College London, London WC1E 6BT, UK
| | - Marc Modat
- Translational Imaging Group, Centre for Medical Image Computing, University College London, London WC1E 6BT, UK
| | - Troy W. Margrie
- The Division of Neurophysiology, MRC National Institute for Medical Research, London NW7 1AA, UK
- The Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK
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26
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Stefaniuk M, Gualda EJ, Pawlowska M, Legutko D, Matryba P, Koza P, Konopka W, Owczarek D, Wawrzyniak M, Loza-Alvarez P, Kaczmarek L. Light-sheet microscopy imaging of a whole cleared rat brain with Thy1-GFP transgene. Sci Rep 2016; 6:28209. [PMID: 27312902 PMCID: PMC4911560 DOI: 10.1038/srep28209] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/31/2016] [Indexed: 12/03/2022] Open
Abstract
Whole-brain imaging with light-sheet fluorescence microscopy and optically cleared tissue is a new, rapidly developing research field. Whereas successful attempts to clear and image mouse brain have been reported, a similar result for rats has proven difficult to achieve. Herein, we report on creating novel transgenic rat harboring fluorescent reporter GFP under control of neuronal gene promoter. We then present data on clearing the rat brain, showing that FluoClearBABB was found superior over passive CLARITY and CUBIC methods. Finally, we demonstrate efficient imaging of the rat brain using light-sheet fluorescence microscopy.
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Affiliation(s)
| | - Emilio J. Gualda
- Institut de Ciencies Fotoniques (ICFO), Barcelona Institute of Science and Technology, 08860, Castelldefels (Barcelona), Spain
| | | | | | | | - Paulina Koza
- Nencki Institute, Pasteura 3, 02-093 Warsaw, Poland
| | | | | | | | - Pablo Loza-Alvarez
- Institut de Ciencies Fotoniques (ICFO), Barcelona Institute of Science and Technology, 08860, Castelldefels (Barcelona), Spain
| | - Leszek Kaczmarek
- Nencki Institute, Pasteura 3, 02-093 Warsaw, Poland
- Institut de Ciencies Fotoniques (ICFO), Barcelona Institute of Science and Technology, 08860, Castelldefels (Barcelona), Spain
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27
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Ghanem A, Conzelmann KK. G gene-deficient single-round rabies viruses for neuronal circuit analysis. Virus Res 2016; 216:41-54. [DOI: 10.1016/j.virusres.2015.05.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/28/2015] [Accepted: 05/31/2015] [Indexed: 12/11/2022]
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28
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Hogstrom LJ, Guo SM, Murugadoss K, Bathe M. Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length scales. Interface Focus 2016; 6:20150081. [PMID: 26855758 DOI: 10.1098/rsfs.2015.0081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Brain function emerges from hierarchical neuronal structure that spans orders of magnitude in length scale, from the nanometre-scale organization of synaptic proteins to the macroscopic wiring of neuronal circuits. Because the synaptic electrochemical signal transmission that drives brain function ultimately relies on the organization of neuronal circuits, understanding brain function requires an understanding of the principles that determine hierarchical neuronal structure in living or intact organisms. Recent advances in fluorescence imaging now enable quantitative characterization of neuronal structure across length scales, ranging from single-molecule localization using super-resolution imaging to whole-brain imaging using light-sheet microscopy on cleared samples. These tools, together with correlative electron microscopy and magnetic resonance imaging at the nanoscopic and macroscopic scales, respectively, now facilitate our ability to probe brain structure across its full range of length scales with cellular and molecular specificity. As these imaging datasets become increasingly accessible to researchers, novel statistical and computational frameworks will play an increasing role in efforts to relate hierarchical brain structure to its function. In this perspective, we discuss several prominent experimental advances that are ushering in a new era of quantitative fluorescence-based imaging in neuroscience along with novel computational and statistical strategies that are helping to distil our understanding of complex brain structure.
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Affiliation(s)
- L J Hogstrom
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - S M Guo
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - K Murugadoss
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - M Bathe
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
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29
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Grinevich V, Knobloch-Bollmann HS, Eliava M, Busnelli M, Chini B. Assembling the Puzzle: Pathways of Oxytocin Signaling in the Brain. Biol Psychiatry 2016; 79:155-64. [PMID: 26001309 DOI: 10.1016/j.biopsych.2015.04.013] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/01/2015] [Accepted: 04/19/2015] [Indexed: 12/24/2022]
Abstract
Oxytocin (OT) is a neuropeptide, which can be seen to be one of the molecules of the decade due to its profound prosocial effects in nonvertebrate and vertebrate species, including humans. Although OT can be detected in various physiological fluids (blood, saliva, urine, cerebrospinal fluid) and brain tissue, it is unclear whether peripheral and central OT releases match and synergize. Moreover, the pathways of OT delivery to brain regions involved in specific behaviors are far from clear. Here, we discuss the evolutionarily and ontogenetically determined pathways of OT delivery and OT signaling, which orchestrate activity of the mesolimbic social decision-making network. Furthermore, we speculate that both the alteration in OT delivery and OT receptor expression may cause behavioral abnormalities in patients afflicted with psychosocial diseases.
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Affiliation(s)
- Valery Grinevich
- Schaller Research Group on Neuropeptides, German Cancer Research Center DKFZ, Heidelberg, Germany; CellNetworks Cluster of Excellence, University of Heidelberg, Heidelberg, Germany.
| | - H Sophie Knobloch-Bollmann
- Schaller Research Group on Neuropeptides, German Cancer Research Center DKFZ, Heidelberg, Germany; CellNetworks Cluster of Excellence, University of Heidelberg, Heidelberg, Germany
| | - Marina Eliava
- Schaller Research Group on Neuropeptides, German Cancer Research Center DKFZ, Heidelberg, Germany; CellNetworks Cluster of Excellence, University of Heidelberg, Heidelberg, Germany
| | - Marta Busnelli
- National Research Council, Institute of Neuroscience, Milan, Italy
| | - Bice Chini
- National Research Council, Institute of Neuroscience, Milan, Italy
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30
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Susaki E, Ueda H. Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals. Cell Chem Biol 2016; 23:137-157. [DOI: 10.1016/j.chembiol.2015.11.009] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 11/20/2015] [Accepted: 11/20/2015] [Indexed: 12/29/2022]
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31
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Sleep as a biological problem: an overview of frontiers in sleep research. J Physiol Sci 2015; 66:1-13. [PMID: 26541158 PMCID: PMC4742504 DOI: 10.1007/s12576-015-0414-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 12/14/2022]
Abstract
Sleep is a physiological process not only for the rest of the body but also for several brain functions such as mood, memory, and consciousness. Nevertheless, the nature and functions of sleep remain largely unknown due to its extremely complicated nature and lack of optimized technology for the experiments. Here we review the recent progress in the biology of the mammalian sleep, which covers a wide range of research areas: the basic knowledge about sleep, the physiology of cerebral cortex in sleeping animals, the detailed morphological features of thalamocortical networks, the mechanisms underlying fluctuating activity of autonomic nervous systems during rapid eye movement sleep, the cutting-edge technology of tissue clearing for visualization of the whole brain, the ketogenesis-mediated homeostatic regulation of sleep, and the forward genetic approach for identification of novel genes involved in sleep. We hope this multifaceted review will be helpful for researchers who are interested in the biology of sleep.
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32
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Lin CW, Lin HW, Chiu MT, Shih YH, Wang TY, Chang HM, Chiang AS. Automated in situ brain imaging for mapping the Drosophila connectome. J Neurogenet 2015. [PMID: 26223305 DOI: 10.3109/01677063.2015.1078801] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mapping the connectome, a wiring diagram of the entire brain, requires large-scale imaging of numerous single neurons with diverse morphology. It is a formidable challenge to reassemble these neurons into a virtual brain and correlate their structural networks with neuronal activities, which are measured in different experiments to analyze the informational flow in the brain. Here, we report an in situ brain imaging technique called Fly Head Array Slice Tomography (FHAST), which permits the reconstruction of structural and functional data to generate an integrative connectome in Drosophila. Using FHAST, the head capsules of an array of flies can be opened with a single vibratome sectioning to expose the brains, replacing the painstaking and inconsistent brain dissection process. FHAST can reveal in situ brain neuroanatomy with minimal distortion to neuronal morphology and maintain intact neuronal connections to peripheral sensory organs. Most importantly, it enables the automated 3D imaging of 100 intact fly brains in each experiment. The established head model with in situ brain neuroanatomy allows functional data to be accurately registered and associated with 3D images of single neurons. These integrative data can then be shared, searched, visualized, and analyzed for understanding how brain-wide activities in different neurons within the same circuit function together to control complex behaviors.
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Affiliation(s)
- Chi-Wen Lin
- a Institute of Biotechnology, National Tsing Hua University , Hsinchu , Taiwan
| | - Hsuan-Wen Lin
- a Institute of Biotechnology, National Tsing Hua University , Hsinchu , Taiwan
| | - Mei-Tzu Chiu
- b Brain Research Center, National Tsing Hua University , Hsinchu , Taiwan
| | - Yung-Hsin Shih
- b Brain Research Center, National Tsing Hua University , Hsinchu , Taiwan
| | - Ting-Yuan Wang
- a Institute of Biotechnology, National Tsing Hua University , Hsinchu , Taiwan
| | - Hsiu-Ming Chang
- b Brain Research Center, National Tsing Hua University , Hsinchu , Taiwan
| | - Ann-Shyn Chiang
- a Institute of Biotechnology, National Tsing Hua University , Hsinchu , Taiwan.,b Brain Research Center, National Tsing Hua University , Hsinchu , Taiwan.,c Genomics Research Center, Academia Sinica , Taipei , Taiwan.,d Department of Biomedical Science and Environmental Biology , Kaohsiung Medical University , Kaohsiung , Taiwan.,e Kavli Institute for Brain and Mind, University of California , San Diego, La Jolla, California , USA
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33
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Schwarz MK, Scherbarth A, Sprengel R, Engelhardt J, Theer P, Giese G. Fluorescent-protein stabilization and high-resolution imaging of cleared, intact mouse brains. PLoS One 2015; 10:e0124650. [PMID: 25993380 PMCID: PMC4439039 DOI: 10.1371/journal.pone.0124650] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/17/2015] [Indexed: 01/15/2023] Open
Abstract
In order to observe and quantify long-range neuronal connections in intact mouse brain by light microscopy, it is first necessary to clear the brain, thus suppressing refractive-index variations. Here we describe a method that clears the brain and preserves the signal from proteinaceous fluorophores using a pH-adjusted non-aqueous index-matching medium. Successful clearing is enabled through the use of either 1-propanol or tert-butanol during dehydration whilst maintaining a basic pH. We show that high-resolution fluorescence imaging of entire, structurally intact juvenile and adult mouse brains is possible at subcellular resolution, even following many months in clearing solution. We also show that axonal long-range projections that are EGFP-labelled by modified Rabies virus can be imaged throughout the brain using a purpose-built light-sheet fluorescence microscope. To demonstrate the viability of the technique, we determined a detailed map of the monosynaptic projections onto a target cell population in the lateral entorhinal cortex. This example demonstrates that our method permits the quantification of whole-brain connectivity patterns at the subcellular level in the uncut brain.
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Affiliation(s)
| | | | - Rolf Sprengel
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Patrick Theer
- Center for Molecular Biology (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Guenter Giese
- Max Planck Institute for Medical Research, Heidelberg, Germany
- * E-mail:
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34
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Pampaloni F, Chang BJ, Stelzer EHK. Light sheet-based fluorescence microscopy (LSFM) for the quantitative imaging of cells and tissues. Cell Tissue Res 2015; 360:129-41. [DOI: 10.1007/s00441-015-2144-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/02/2015] [Indexed: 01/04/2023]
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35
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Eberle AL, Selchow O, Thaler M, Zeidler D, Kirmse R. Mission (im)possible – mapping the brain becomes a reality. Microscopy (Oxf) 2014; 64:45-55. [DOI: 10.1093/jmicro/dfu104] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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Imai T. Construction of functional neuronal circuitry in the olfactory bulb. Semin Cell Dev Biol 2014; 35:180-8. [PMID: 25084319 DOI: 10.1016/j.semcdb.2014.07.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/11/2014] [Accepted: 07/17/2014] [Indexed: 11/29/2022]
Abstract
Recent studies using molecular genetics, electrophysiology, in vivo imaging, and behavioral analyses have elucidated detailed connectivity and function of the mammalian olfactory circuits. The olfactory bulb is the first relay station of olfactory perception in the brain, but it is more than a simple relay: olfactory information is dynamically tuned by local olfactory bulb circuits and converted to spatiotemporal neural code for higher-order information processing. Because the olfactory bulb processes ∼1000 discrete input channels from different odorant receptors, it serves as a good model to study neuronal wiring specificity, from both functional and developmental aspects. This review summarizes our current understanding of the olfactory bulb circuitry from functional standpoint and discusses important future studies with particular focus on its development and plasticity.
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Affiliation(s)
- Takeshi Imai
- Laboratory for Sensory Circuit Formation, RIKEN Center for Developmental Biology, Kobe, Japan; PRESTO, Japan Science and Technology Agency, Saitama, Japan.
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37
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Abstract
One of the most fascinating challenges in neuroscience is the reconstruction of the connectivity map of the brain. Recent years have seen a rapid expansion in the field of connectomics, whose aim is to trace this map and understand its relationship with neural computation. Many different approaches, ranging from electron and optical microscopy to magnetic resonance imaging, have been proposed to address the connectomics challenge on various spatial scales and in different species. Here, we review the main technological advances in the microscopy techniques applied to connectomics, highlighting the potential and limitations of the different methods. Finally, we briefly discuss the role of connectomics in the Human Brain Project, the Future and Emerging Technologies (FET) Flagship recently approved by the European Commission.
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38
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Wu Y, Christensen R, Colón-Ramos D, Shroff H. Advanced optical imaging techniques for neurodevelopment. Curr Opin Neurobiol 2013; 23:1090-7. [PMID: 23831260 PMCID: PMC3830703 DOI: 10.1016/j.conb.2013.06.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/12/2013] [Accepted: 06/13/2013] [Indexed: 01/27/2023]
Abstract
Over the past decade, developmental neuroscience has been transformed by the widespread application of confocal and two-photon fluorescence microscopy. Even greater progress is imminent, as recent innovations in microscopy now enable imaging with increased depth, speed, and spatial resolution; reduced phototoxicity; and in some cases without external fluorescent probes. We discuss these new techniques and emphasize their dramatic impact on neurobiology, including the ability to image neurons at depths exceeding 1mm, to observe neurodevelopment noninvasively throughout embryogenesis, and to visualize neuronal processes or structures that were previously too small or too difficult to target with conventional microscopy.
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Affiliation(s)
- Yicong Wu
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bethesda, MD 20892
| | - Ryan Christensen
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06536
| | - Daniel Colón-Ramos
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06536
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bethesda, MD 20892
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39
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Osten P, Margrie TW. Mapping brain circuitry with a light microscope. Nat Methods 2013; 10:515-23. [PMID: 23722211 PMCID: PMC3982327 DOI: 10.1038/nmeth.2477] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 04/15/2013] [Indexed: 12/16/2022]
Abstract
The beginning of the 21st century has seen a renaissance in light microscopy and anatomical tract tracing that together are rapidly advancing our understanding of the form and function of neuronal circuits. The introduction of instruments for automated imaging of whole mouse brains, new cell type–specific and trans-synaptic tracers, and computational methods for handling the whole-brain data sets has opened the door to neuroanatomical studies at an unprecedented scale. We present an overview of the present state and future opportunities in charting long-range and local connectivity in the entire mouse brain and in linking brain circuits to function.
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Affiliation(s)
- Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
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40
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Brunjes PC. The mouse olfactory peduncle. 2.The anterior limb of the anterior commissure. Front Neuroanat 2013; 6:51. [PMID: 23355812 PMCID: PMC3555037 DOI: 10.3389/fnana.2012.00051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 12/28/2012] [Indexed: 11/17/2022] Open
Abstract
The central core of the olfactory peduncle [the tissue connecting the olfactory bulb (OB) to the forebrain] includes a white matter tract that extends caudally to the anterior commissure (AC). The purpose of the present study was to examine this “anterior limb of the anterior commissure” (ALAC) to determine if the axons that progress through it segregate on the basis of their point of origin, neurotransmitter type, size, or shape. While local differences in axon density were observed in the ALAC, they were not consistent between samples of the anterior and posterior peduncle, and no other compartmentalization within the tract was observed. The innervation of the caudal olfactory peduncle by neuromodulatory fibers was examined to determine if they enter the region via the ALAC. Cholinergic fibers (CHAT) densely filled the peduncle, followed in order by serotonergic, noradrenergic, histaminergic, and orexinergic processes. Differences in the distribution of the fibers were noted for each system. While each axon type could be observed in the ALAC, it is probable that they enter the peduncle though several routes. Data for axon caliber in the ALAC was compared to information previously collected on the peduncle's other white matter region, the lateral olfactory tract (LOT). Axons in the ALAC were smaller, suggesting that the olfactory system is organized with a fast system for distributing incoming sensory information and a more economical, distributed system for subsequent processing.
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Affiliation(s)
- Peter C Brunjes
- Department of Psychology, University of Virginia Charlottesville, VA, USA
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