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Erboz A, Kesekler E, Gentili PL, Uversky VN, Coskuner-Weber O. Electromagnetic radiation and biophoton emission in neuronal communication and neurodegenerative diseases. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2025; 195:87-99. [PMID: 39732343 DOI: 10.1016/j.pbiomolbio.2024.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 12/08/2024] [Accepted: 12/24/2024] [Indexed: 12/30/2024]
Abstract
The intersection of electromagnetic radiation and neuronal communication, focusing on the potential role of biophoton emission in brain function and neurodegenerative diseases is an emerging research area. Traditionally, it is believed that neurons encode and communicate information via electrochemical impulses, generating electromagnetic fields detectable by EEG and MEG. Recent discoveries indicate that neurons may also emit biophotons, suggesting an additional communication channel alongside the regular synaptic interactions. This dual signaling system is analyzed for its potential in synchronizing neuronal activity and improving information transfer, with implications for brain-like computing systems. The clinical relevance is explored through the lens of neurodegenerative diseases and intrinsically disordered proteins, where oxidative stress may alter biophoton emission, offering clues for pathological conditions, such as Alzheimer's and Parkinson's diseases. The potential therapeutic use of Low-Level Laser Therapy (LLLT) is also examined for its ability to modulate biophoton activity and mitigate oxidative stress, presenting new opportunities for treatment. Here, we invite further exploration into the intricate roles the electromagnetic phenomena play in brain function, potentially leading to breakthroughs in computational neuroscience and medical therapies for neurodegenerative diseases.
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Affiliation(s)
- Aysin Erboz
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi No. 106, Beykoz, Istanbul, 34820, Turkey
| | - Elif Kesekler
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi No. 106, Beykoz, Istanbul, 34820, Turkey
| | - Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, Università degli Studi di Perugia, 06123, Perugia, Italy.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA.
| | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi No. 106, Beykoz, Istanbul, 34820, Turkey.
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2
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Collins LT, Huffman T, Koene R. Comparative prospects of imaging methods for whole-brain mammalian connectomics. CELL REPORTS METHODS 2025; 5:100988. [PMID: 39970909 PMCID: PMC11955263 DOI: 10.1016/j.crmeth.2025.100988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Revised: 12/02/2024] [Accepted: 01/27/2025] [Indexed: 02/21/2025]
Abstract
Mammalian whole-brain connectomes are a foundational ingredient for a holistic understanding of brains. Indeed, imaging connectomes at sufficient resolution to densely reconstruct cellular morphology and synapses represents a long-standing goal in neuroscience. Mouse connectomes could soon come within reach, while human connectomes remain a more distant yet still worthy goal. Though the technologies needed to reconstruct whole-brain connectomes have not yet reached full maturity, they are advancing rapidly. Close examination of these technologies may help plan connectomics projects. Here, we quantitatively compare imaging technologies that have the potential to enable whole-brain mammalian connectomics. We perform calculations on electron microscopy (EM) techniques and expansion light-sheet fluorescence microscopy (ExLSFM) methods. We consider techniques that have sufficient resolution to identify all synapses and sufficient speed to be relevant for whole mammalian brains. We offer this analysis as a resource for those considering how to organize efforts toward imaging whole-brain mammalian connectomes.
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Affiliation(s)
- Logan Thrasher Collins
- Washington University in St. Louis, Department of Biomedical Engineering, St. Louis, MO, USA.
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3
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Jia D, Cui M, Divsalar A, Khattab TA, Al-Qahtani SD, Cheung E, Ding X. Derivative Technologies of Expansion Microscopy and Applications in Biomedicine. Chembiochem 2025; 26:e202400795. [PMID: 39681518 DOI: 10.1002/cbic.202400795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 11/20/2024] [Accepted: 12/16/2024] [Indexed: 12/18/2024]
Abstract
Expansion microscopy (ExM) is an innovative super-resolution imaging technique that utilizes physical expansion to magnify biological samples, facilitating the visualization of cellular structures that are challenging to observe using traditional optical microscopes. The fundamental principle of ExM revolves around employing a specialized hydrogel to uniformly expand biological samples, thereby achieving super-resolution imaging under conventional optical imaging conditions. This technology finds application not only in various biological samples such as cells and tissue sections, but also enables super-resolution imaging of large biological molecules including proteins, nucleic acids, and metabolite molecules. In recent years, numerous researchers have delved into ExM, resulting in the continuous development of a range of derivative technologies that optimize experimental protocols and broaden practical application fields. This article presents a comprehensive review of these derivative technologies, highlighting the utilization of ExM for anchoring nucleic acids, proteins, and other biological molecules, as well as its applications in biomedicine. Furthermore, this review offers insights into the future development prospects of ExM technology.
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Affiliation(s)
- Dongling Jia
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Minhui Cui
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Adeleh Divsalar
- Department of Cell & Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, 15719-14911, Iran
| | - Tawfik A Khattab
- Dyeing, Printing and Auxiliaries Department, Textile Research and Technology Institute National Research Centre, Cairo, 12622, Egypt
| | - Salhah D Al-Qahtani
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Edwin Cheung
- Cancer Centre, Centre for Precision Medicine Research and Training, Faculty of Health Science, University of Macau Taipa, 999078, Macau, SAR
| | - Xianting Ding
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
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4
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Shin TW, Wang H, Zhang C, An B, Lu Y, Zhang E, Lu X, Karagiannis ED, Kang JS, Emenari A, Symvoulidis P, Asano S, Lin L, Costa EK, Marblestone AH, Kasthuri N, Tsai LH, Boyden ES. Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues. Nat Commun 2025; 16:1579. [PMID: 39939319 PMCID: PMC11821914 DOI: 10.1038/s41467-025-56641-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 01/24/2025] [Indexed: 02/14/2025] Open
Abstract
Lipid membranes are key to the nanoscale compartmentalization of biological systems, but fluorescent visualization of them in intact tissues, with nanoscale precision, is challenging to do with high labeling density. Here, we report ultrastructural membrane expansion microscopy (umExM), which combines an innovative membrane label and optimized expansion microscopy protocol, to support dense labeling of membranes in tissues for nanoscale visualization. We validate the high signal-to-background ratio, and uniformity and continuity, of umExM membrane labeling in brain slices, which supports the imaging of membranes and proteins at a resolution of ~60 nm on a confocal microscope. We demonstrate the utility of umExM for the segmentation and tracing of neuronal processes, such as axons, in mouse brain tissue. Combining umExM with optical fluctuation imaging, or iterating the expansion process, yields ~35 nm resolution imaging, pointing towards the potential for electron microscopy resolution visualization of brain membranes on ordinary light microscopes.
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Affiliation(s)
- Tay Won Shin
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02140, USA
| | - Hao Wang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chi Zhang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bobae An
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yangning Lu
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Elizabeth Zhang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Xiaotang Lu
- Department of Cellular and Molecular Biology, Harvard University, Cambridge, MA, 02138, USA
| | | | - Jeong Seuk Kang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Amauche Emenari
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Shoh Asano
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Pfizer Inc, Cambridge, MA, 02139, USA
| | - Leanne Lin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Emma K Costa
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Adam H Marblestone
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Convergent Research, Cambridge, MA, 02140, USA
| | - Narayanan Kasthuri
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, 60439, USA
- Department of Neurobiology, University of Chicago, Chicago, IL, 60637, USA
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Edward S Boyden
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02140, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- K. Lisa Yang Center for Bionics, Cambridge, MA, 02139, USA.
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA.
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5
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Micheva KD, Simhal AK, Schardt J, Smith SJ, Weinberg RJ, Owen SF. Data-driven synapse classification reveals a logic of glutamate receptor diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.12.11.628056. [PMID: 39713368 PMCID: PMC11661198 DOI: 10.1101/2024.12.11.628056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
The rich diversity of synapses facilitates the capacity of neural circuits to transmit, process and store information. We used multiplex super-resolution proteometric imaging through array tomography to define features of single synapses in mouse neocortex. We find that glutamatergic synapses cluster into subclasses that parallel the distinct biochemical and functional categories of receptor subunits: GluA1/4, GluA2/3 and GluN1/GluN2B. Two of these subclasses align with physiological expectations based on synaptic plasticity: large AMPAR-rich synapses may represent potentiated synapses, whereas small NMDAR-rich synapses suggest "silent" synapses. The NMDA receptor content of large synapses correlates with spine neck diameter, and thus the potential for coupling to the parent dendrite. Overall, ultrastructural features predict receptor content of synapses better than parent neuron identity does, suggesting synapse subclasses act as fundamental elements of neuronal circuits. No barriers prevent future generalization of this approach to other species, or to study of human disorders and therapeutics.
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Affiliation(s)
- Kristina D. Micheva
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Anish K. Simhal
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Jenna Schardt
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Stephen J Smith
- Allen Institute for Brain Science, Seattle, WA 98109
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | - Richard J. Weinberg
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27514
| | - Scott F. Owen
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305
- Lead contact
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6
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Kang J, Schroeder ME, Lee Y, Kapoor C, Yu E, Tarr TB, Titterton K, Zeng M, Park D, Niederst E, Wei D, Feng G, Boyden ES. Multiplexed expansion revealing for imaging multiprotein nanostructures in healthy and diseased brain. Nat Commun 2024; 15:9722. [PMID: 39521775 PMCID: PMC11550395 DOI: 10.1038/s41467-024-53729-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/21/2024] [Indexed: 11/16/2024] Open
Abstract
Proteins work together in nanostructures in many physiological contexts and disease states. We recently developed expansion revealing (ExR), which expands proteins away from each other, in order to support better labeling with antibody tags and nanoscale imaging on conventional microscopes. Here, we report multiplexed expansion revealing (multiExR), which enables high-fidelity antibody visualization of >20 proteins in the same specimen, over serial rounds of staining and imaging. Across all datasets examined, multiExR exhibits a median round-to-round registration error of 39 nm, with a median registration error of 25 nm when the most stringent form of the protocol is used. We precisely map 23 proteins in the brain of 5xFAD Alzheimer's model mice, and find reductions in synaptic protein cluster volume, and co-localization of specific AMPA receptor subunits with amyloid-beta nanoclusters. We visualize 20 synaptic proteins in specimens of mouse primary somatosensory cortex. multiExR may be of broad use in analyzing how different kinds of protein are organized amidst normal and pathological processes in biology.
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Affiliation(s)
- Jinyoung Kang
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Yang Tan Collective, MIT, Cambridge, MA, USA
| | - Margaret E Schroeder
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Youngmi Lee
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Chaitanya Kapoor
- Department of Electrical and Electronics Engineering, BITS Pilani, Rajasthan, India
| | - Eunah Yu
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Tyler B Tarr
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kat Titterton
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Menglong Zeng
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Demian Park
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Emily Niederst
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
| | - Donglai Wei
- Department of Computer Science, Boston College, Chestnut Hill, MA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Yang Tan Collective, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edward S Boyden
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA.
- Yang Tan Collective, MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
- Center for Neurobiological Engineering and K. Lisa Yang Center for Bionics, MIT, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- Koch Institute, MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
- Media Arts and Sciences, MIT, Cambridge, MA, USA.
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7
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Yao L, Zhang L, Chen L, Fei Y, Lamon S, Gu M, Mi L, Wang J, Ma J. Visualizing highly bright and uniform cellular ultrastructure by expansion-microscopy with tetrahedral DNA nanostructures. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 260:113034. [PMID: 39288552 DOI: 10.1016/j.jphotobiol.2024.113034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 08/24/2024] [Accepted: 09/09/2024] [Indexed: 09/19/2024]
Abstract
Expansion Microscopy (ExM) is a widely used super-resolution technique that enables imaging of structures beyond the diffraction limit of light. However, ExM suffers from weak labeling signals and expansion distortions, limiting its applicability. Here, we present an innovative approach called Tetrahedral DNA nanostructure Expansion Microscopy (TDN-ExM), addressing these limitations by using tetrahedral DNA nanostructures (TDNs) for fluorescence labeling. Our approach demonstrates a 3- to 10-fold signal amplification due to the multivertex nature of TDNs, allowing the modification of multiple dyes. Previous studies have confirmed minimal distortion on a large scale, and our strategy can reduce the distortion at the ultrastructural level in samples because it does not rely on anchoring agents and is not affected by digestion. This results in a brighter fluorescence, better uniformity, and compatibility with different labeling strategies and optical super-resolution technologies. We validated the utility of TDN-ExM by imaging various biological structures with improved resolutions and signal-to-noise ratios.
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Affiliation(s)
- Longfang Yao
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai 200093, China; Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Li Zhang
- Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems (MRICS), School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Liwen Chen
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Simone Lamon
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai 200093, China
| | - Min Gu
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai 200093, China
| | - Lan Mi
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Jing Wang
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai 200093, China.
| | - Jiong Ma
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, 220 Handan Road, Shanghai 200433, China; Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems (MRICS), School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.
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8
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Saadh MJ, Shallan MA, Hussein UAR, Mohammed AQ, Al-Shuwaili SJ, Shikara M, Ami AA, Khalil NAMA, Ahmad I, Abbas HH, Elawady A. Advances in microscopy characterization techniques for lipid nanocarriers in drug delivery: a comprehensive review. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:5463-5481. [PMID: 38459989 DOI: 10.1007/s00210-024-03033-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/28/2024] [Indexed: 03/11/2024]
Abstract
This review paper provides an in-depth analysis of the significance of lipid nanocarriers in drug delivery and the crucial role of characterization techniques. It explores various types of lipid nanocarriers and their applications, emphasizing the importance of microscopy-based characterization methods such as light microscopy, confocal microscopy, transmission electron microscopy (TEM), scanning electron microscopy (SEM), and atomic force microscopy (AFM). The paper also delves into sample preparation, quantitative analysis, challenges, and future directions in the field. The review concludes by underlining the pivotal role of microscopy-based characterization in advancing lipid nanocarrier research and drug delivery technologies.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman, 11831, Jordan
| | | | | | | | | | | | - Ahmed Ali Ami
- Department of Medical Laboratories Technology, Al-Nisour University College, Baghdad, Iraq
| | | | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, King Khalid University, Abha, Saudi Arabia
| | - Huda Hayder Abbas
- College of Pharmacy, National University of Science and Technology, Dhi Qar, Iraq
| | - Ahmed Elawady
- College of Technical Engineering, The Islamic University, Najaf, Iraq.
- College of Technical Engineering, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq.
- College of Technical Engineering, The Islamic University of Babylon, Babylon, Iraq.
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9
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Delhaye M, LeDue J, Robinson K, Xu Q, Zhang Q, Oku S, Zhang P, Craig AM. Adaptation of Magnified Analysis of the Proteome for Excitatory Synaptic Proteins in Varied Samples and Evaluation of Cell Type-Specific Distributions. J Neurosci 2024; 44:e1291232024. [PMID: 38360747 PMCID: PMC10993037 DOI: 10.1523/jneurosci.1291-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024] Open
Abstract
Growing evidence suggests a remarkable diversity and complexity in the molecular composition of synapses, forming the basis for the brain to execute complex behaviors. Hence, there is considerable interest in visualizing the spatial distribution of such molecular diversity at individual synapses within intact brain circuits. Yet this task presents significant technical challenges. Expansion microscopy approaches have revolutionized our view of molecular anatomy. However, their use to study synapse-related questions outside of the labs developing them has been limited. Here we independently adapted a version of Magnified Analysis of the Proteome (MAP) and present a step-by-step protocol for visualizing over 40 synaptic proteins in brain circuits. Surprisingly, our findings show that the advantage of MAP over conventional immunolabeling was primarily due to improved antigen recognition and secondarily physical expansion. Furthermore, we demonstrated the versatile use of MAP in brains perfused with paraformaldehyde or fresh-fixed with formalin and in formalin-fixed paraffin-embedded tissue. These tests expand the potential applications of MAP to combinations with slice electrophysiology or clinical pathology specimens. Using male and female mice expressing YFP-ChR2 exclusively in interneurons, we revealed a distinct composition of AMPA and NMDA receptors and Shank family members at synapses on hippocampal interneurons versus on pyramidal neurons. Quantitative single synapse analyses yielded comprehensive cell type distributions of synaptic proteins and their relationships. These findings exemplify the value of the versatile adapted MAP procedure presented here as an accessible tool for the broad neuroscience community to unravel the complexity of the "synaptome" across brain circuits and disease states.
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Affiliation(s)
- Mathias Delhaye
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Jeffrey LeDue
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Kaylie Robinson
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Qin Xu
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Qian Zhang
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Shinichiro Oku
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Peng Zhang
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Ann Marie Craig
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
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10
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Valdes PA, Yu CC(J, Aronson J, Ghosh D, Zhao Y, An B, Bernstock JD, Bhere D, Felicella MM, Viapiano MS, Shah K, Chiocca EA, Boyden ES. Improved immunostaining of nanostructures and cells in human brain specimens through expansion-mediated protein decrowding. Sci Transl Med 2024; 16:eabo0049. [PMID: 38295184 PMCID: PMC10911838 DOI: 10.1126/scitranslmed.abo0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
Proteins are densely packed in cells and tissues, where they form complex nanostructures. Expansion microscopy (ExM) variants have been used to separate proteins from each other in preserved biospecimens, improving antibody access to epitopes. Here, we present an ExM variant, decrowding expansion pathology (dExPath), that can expand proteins away from each other in human brain pathology specimens, including formalin-fixed paraffin-embedded (FFPE) clinical specimens. Immunostaining of dExPath-expanded specimens reveals, with nanoscale precision, previously unobserved cellular structures, as well as more continuous patterns of staining. This enhanced molecular staining results in observation of previously invisible disease marker-positive cell populations in human glioma specimens, with potential implications for tumor aggressiveness. dExPath results in improved fluorescence signals even as it eliminates lipofuscin-associated autofluorescence. Thus, this form of expansion-mediated protein decrowding may, through improved epitope access for antibodies, render immunohistochemistry more powerful in clinical science and, perhaps, diagnosis.
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Affiliation(s)
- Pablo A. Valdes
- Department of Neurosurgery, University of Texas Medical Branch, Galveston, TX, 77555
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
| | - Chih-Chieh (Jay) Yu
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Engineering, MIT, MA, USA, 02139
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- RIKEN Center for Brain Science, Saitama, Japan, 351-0198
| | - Jenna Aronson
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- RIKEN Center for Brain Science, Saitama, Japan, 351-0198
| | - Debarati Ghosh
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA, 02139
| | - Yongxin Zhao
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA, 15213
| | - Bobae An
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
| | - Joshua D. Bernstock
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Koch Institute, MIT, Cambridge, MA, USA, 02139
| | - Deepak Bhere
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Department of Pathology, Microbiology and Immunology, School of Medicine Columbia, University of South Carolina, Columbia, SC, USA, 29209
- Center for Stem Cell and Translational Immunotherapy, Harvard Medical School/Brigham and Women’s Hospital, Boston, MA, USA, 02115
| | - Michelle M. Felicella
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA, 77555
| | - Mariano S. Viapiano
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA, 13210
| | - Khalid Shah
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Center for Stem Cell and Translational Immunotherapy, Harvard Medical School/Brigham and Women’s Hospital, Boston, MA, USA, 02115
| | - E. Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Edward S. Boyden
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Engineering, MIT, MA, USA, 02139
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA, 02139
- Koch Institute, MIT, Cambridge, MA, USA, 02139
- MIT Center for Neurobiological Engineering and K. Lisa Yang Center for Bionics, MIT, Cambridge, MA, USA, 02139
- Howard Hughes Medical Institute, Cambridge, MA, USA, 02139
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11
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Wang Z, Zhang J, Symvoulidis P, Guo W, Zhang L, Wilson MA, Boyden ES. Imaging the voltage of neurons distributed across entire brains of larval zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571964. [PMID: 38168290 PMCID: PMC10760087 DOI: 10.1101/2023.12.15.571964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Neurons interact in networks distributed throughout the brain. Although much effort has focused on whole-brain calcium imaging, recent advances in genetically encoded voltage indicators (GEVIs) raise the possibility of imaging voltage of neurons distributed across brains. To achieve this, a microscope must image at high volumetric rate and signal-to-noise ratio. We present a remote scanning light-sheet microscope capable of imaging GEVI-expressing neurons distributed throughout entire brains of larval zebrafish at a volumetric rate of 200.8 Hz. We measured voltage of ∼1/3 of the neurons of the brain, distributed throughout. We observed that neurons firing at different times during a sequence were located at different brain locations, for sequences elicited by a visual stimulus, which mapped onto locations throughout the optic tectum, as well as during stimulus-independent bursts, which mapped onto locations in the cerebellum and medulla. Whole-brain voltage imaging may open up frontiers in the fundamental operation of neural systems.
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12
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Blot FGC, White JJ, van Hattem A, Scotti L, Balaji V, Adolfs Y, Pasterkamp RJ, De Zeeuw CI, Schonewille M. Purkinje cell microzones mediate distinct kinematics of a single movement. Nat Commun 2023; 14:4358. [PMID: 37468512 PMCID: PMC10356806 DOI: 10.1038/s41467-023-40111-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/12/2023] [Indexed: 07/21/2023] Open
Abstract
The classification of neuronal subpopulations has significantly advanced, yet its relevance for behavior remains unclear. The highly organized flocculus of the cerebellum, known to fine-tune multi-axial eye movements, is an ideal substrate for the study of potential functions of neuronal subpopulations. Here, we demonstrate that its recently identified subpopulations of 9+ and 9- Purkinje cells exhibit an intermediate Aldolase C expression and electrophysiological profile, providing evidence for a graded continuum of intrinsic properties among PC subpopulations. By identifying and utilizing two Cre-lines that genetically target these floccular domains, we show with high spatial specificity that these subpopulations of Purkinje cells participate in separate micromodules with topographically organized connections. Finally, optogenetic excitation of the respective subpopulations results in movements around the same axis in space, yet with distinct kinematic profiles. These results indicate that Purkinje cell subpopulations integrate in discrete circuits and mediate particular parameters of single movements.
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Affiliation(s)
| | - Joshua J White
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Amy van Hattem
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Licia Scotti
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Vaishnavi Balaji
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Youri Adolfs
- Department of Translational Neuroscience, University Medical Center Utrecht, Brain Center, Utrecht University, Utrecht, The Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, University Medical Center Utrecht, Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Chris I De Zeeuw
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, Netherlands
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13
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Liu Y, Shen X, Zhang Y, Zheng X, Cepeda C, Wang Y, Duan S, Tong X. Interactions of glial cells with neuronal synapses, from astrocytes to microglia and oligodendrocyte lineage cells. Glia 2023; 71:1383-1401. [PMID: 36799296 DOI: 10.1002/glia.24343] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 02/18/2023]
Abstract
The mammalian brain is a complex organ comprising neurons, glia, and more than 1 × 1014 synapses. Neurons are a heterogeneous group of electrically active cells, which form the framework of the complex circuitry of the brain. However, glial cells, which are primarily divided into astrocytes, microglia, oligodendrocytes (OLs), and oligodendrocyte precursor cells (OPCs), constitute approximately half of all neural cells in the mammalian central nervous system (CNS) and mainly provide nutrition and tropic support to neurons in the brain. In the last two decades, the concept of "tripartite synapses" has drawn great attention, which emphasizes that astrocytes are an integral part of the synapse and regulate neuronal activity in a feedback manner after receiving neuronal signals. Since then, synaptic modulation by glial cells has been extensively studied and substantially revised. In this review, we summarize the latest significant findings on how glial cells, in particular, microglia and OL lineage cells, impact and remodel the structure and function of synapses in the brain. Our review highlights the cellular and molecular aspects of neuron-glia crosstalk and provides additional information on how aberrant synaptic communication between neurons and glia may contribute to neural pathologies.
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Affiliation(s)
- Yao Liu
- Songjiang Institute and Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi Shen
- Songjiang Institute and Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhan Zhang
- College of Basic Medical Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoli Zheng
- Songjiang Institute and Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Carlos Cepeda
- Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Yao Wang
- Department of Assisted Reproduction, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shumin Duan
- Songjiang Institute and Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, State Key Laboratory of Brain-Machine Intelligence, Zhejiang University, Hangzhou, China
| | - Xiaoping Tong
- Songjiang Institute and Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, China
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14
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Walker LA, McGlothlin M, Li Y, Cai D. A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525380. [PMID: 36747668 PMCID: PMC9900847 DOI: 10.1101/2023.01.24.525380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Modern high-throughput microscopy methods such as light-sheet imaging and electron microscopy are capable of producing petabytes of data inside of a single experiment. Storage of these large images, however, is challenging because of the difficulty of moving, storing, and analyzing such vast amounts of data, which is often collected at very high data rates (>1GBps). In this report, we provide a comparison of the performance of several compression algorithms using a collection of published and unpublished datasets including confocal, fMOST, and pathology images. We also use simulated data to demonstrate the efficiency of each algorithm as image content or entropy increases. As a result of this work, we recommend the use of the BLOSC algorithm combined with ZSTD for various microscopy applications, as it produces the best compression ratio over a collection of conditions.
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Affiliation(s)
| | | | - Ye Li
- University of Michigan, Ann Arbor, Michigan, USA
| | - Dawen Cai
- University of Michigan, Ann Arbor, Michigan, USA
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15
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Barker CM, Miles KD, Doll CA. Fmrp regulates neuronal balance in embryonic motor circuit formation. Front Neurosci 2022; 16:962901. [PMID: 36408418 PMCID: PMC9669763 DOI: 10.3389/fnins.2022.962901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Motor behavior requires the balanced production and integration of a variety of neural cell types. Motor neurons are positioned in discrete locations in the spinal cord, targeting specific muscles to drive locomotive contractions. Specialized spinal interneurons modulate and synchronize motor neuron activity to achieve coordinated motor output. Changes in the ratios and connectivity of spinal interneurons could drastically alter motor output by tipping the balance of inhibition and excitation onto target motor neurons. Importantly, individuals with Fragile X syndrome (FXS) and associated autism spectrum disorders often have significant motor challenges, including repetitive behaviors and epilepsy. FXS stems from the transcriptional silencing of the gene Fragile X Messenger Ribonucleoprotein 1 (FMR1), which encodes an RNA binding protein that is implicated in a multitude of crucial neurodevelopmental processes, including cell specification. Our work shows that Fmrp regulates the formation of specific interneurons and motor neurons that comprise early embryonic motor circuits. We find that zebrafish fmr1 mutants generate surplus ventral lateral descending (VeLD) interneurons, an early-born cell derived from the motor neuron progenitor domain (pMN). As VeLD interneurons are hypothesized to act as central pattern generators driving the earliest spontaneous movements, this imbalance could influence the formation and long-term function of motor circuits driving locomotion. fmr1 embryos also show reduced expression of proteins associated with inhibitory synapses, including the presynaptic transporter vGAT and the postsynaptic scaffold Gephyrin. Taken together, we show changes in embryonic motor circuit formation in fmr1 mutants that could underlie persistent hyperexcitability.
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Affiliation(s)
- Chase M. Barker
- Section of Developmental Biology, Department of Pediatrics, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, CO, United States
| | - Kaleb D. Miles
- Section of Developmental Biology, Department of Pediatrics, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, CO, United States
- Biomedical Sciences and Biotechnology Program, Graduate School, University of Colorado, Aurora, CO, United States
| | - Caleb A. Doll
- Section of Developmental Biology, Department of Pediatrics, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, CO, United States
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16
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Multicolor strategies for investigating clonal expansion and tissue plasticity. Cell Mol Life Sci 2022; 79:141. [PMID: 35187598 PMCID: PMC8858928 DOI: 10.1007/s00018-021-04077-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/27/2021] [Accepted: 10/14/2021] [Indexed: 12/20/2022]
Abstract
Understanding the generation of complexity in living organisms requires the use of lineage tracing tools at a multicellular scale. In this review, we describe the different multicolor strategies focusing on mouse models expressing several fluorescent reporter proteins, generated by classical (MADM, Brainbow and its multiple derivatives) or acute (StarTrack, CLoNe, MAGIC Markers, iOn, viral vectors) transgenesis. After detailing the multi-reporter genetic strategies that serve as a basis for the establishment of these multicolor mouse models, we briefly mention other animal and cellular models (zebrafish, chicken, drosophila, iPSC) that also rely on these constructs. Then, we highlight practical applications of multicolor mouse models to better understand organogenesis at single progenitor scale (clonal analyses) in the brain and briefly in several other tissues (intestine, skin, vascular, hematopoietic and immune systems). In addition, we detail the critical contribution of multicolor fate mapping strategies in apprehending the fine cellular choreography underlying tissue morphogenesis in several models with a particular focus on brain cytoarchitecture in health and diseases. Finally, we present the latest technological advances in multichannel and in-depth imaging, and automated analyses that enable to better exploit the large amount of data generated from multicolored tissues.
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17
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Sneve MA, Piatkevich KD. Towards a Comprehensive Optical Connectome at Single Synapse Resolution via Expansion Microscopy. Front Synaptic Neurosci 2022; 13:754814. [PMID: 35115916 PMCID: PMC8803729 DOI: 10.3389/fnsyn.2021.754814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/17/2021] [Indexed: 12/04/2022] Open
Abstract
Mapping and determining the molecular identity of individual synapses is a crucial step towards the comprehensive reconstruction of neuronal circuits. Throughout the history of neuroscience, microscopy has been a key technology for mapping brain circuits. However, subdiffraction size and high density of synapses in brain tissue make this process extremely challenging. Electron microscopy (EM), with its nanoscale resolution, offers one approach to this challenge yet comes with many practical limitations, and to date has only been used in very small samples such as C. elegans, tadpole larvae, fruit fly brain, or very small pieces of mammalian brain tissue. Moreover, EM datasets require tedious data tracing. Light microscopy in combination with tissue expansion via physical magnification-known as expansion microscopy (ExM)-offers an alternative approach to this problem. ExM enables nanoscale imaging of large biological samples, which in combination with multicolor neuronal and synaptic labeling offers the unprecedented capability to trace and map entire neuronal circuits in fully automated mode. Recent advances in new methods for synaptic staining as well as new types of optical molecular probes with superior stability, specificity, and brightness provide new modalities for studying brain circuits. Here we review advanced methods and molecular probes for fluorescence staining of the synapses in the brain that are compatible with currently available expansion microscopy techniques. In particular, we will describe genetically encoded probes for synaptic labeling in mice, zebrafish, Drosophila fruit flies, and C. elegans, which enable the visualization of post-synaptic scaffolds and receptors, presynaptic terminals and vesicles, and even a snapshot of the synaptic activity itself. We will address current methods for applying these probes in ExM experiments, as well as appropriate vectors for the delivery of these molecular constructs. In addition, we offer experimental considerations and limitations for using each of these tools as well as our perspective on emerging tools.
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Affiliation(s)
- Madison A. Sneve
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, United States
| | - Kiryl D. Piatkevich
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
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18
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Eckermann M, van der Meer F, Cloetens P, Ruhwedel T, Möbius W, Stadelmann C, Salditt T. Three-dimensional virtual histology of the cerebral cortex based on phase-contrast X-ray tomography. BIOMEDICAL OPTICS EXPRESS 2021; 12:7582-7598. [PMID: 35003854 PMCID: PMC8713656 DOI: 10.1364/boe.434885] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 05/09/2023]
Abstract
In this work, we optimize the setups and experimental parameters of X-ray phase-contrast computed-tomography for the three-dimensional imaging of the cyto- and myeloarchitecture of cerebral cortex, including both human and murine tissue. We present examples for different optical configurations using state-of-the art synchrotron instruments for holographic tomography, as well as compact laboratory setups for phase-contrast tomography in the direct contrast (edge-enhancement) regime. Apart from unstained and paraffin-embedded tissue, we tested hydrated tissue, as well as heavy metal stained and resin-embedded tissue using two different protocols. Further, we show that the image quality achieved allows to assess the neuropathology of multiple sclerosis in a biopsy sample collected during surgery.
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Affiliation(s)
- Marina Eckermann
- Institut für Röntgenphysik, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
| | | | - Peter Cloetens
- ESRF, the European Synchrotron, 71, avenue des Martyrs, 38043 Grenoble Cedex 9, France
| | - Torben Ruhwedel
- Max-Planck-Institut für experimentelle Medizin, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Wiebke Möbius
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Max-Planck-Institut für experimentelle Medizin, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Christine Stadelmann
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Institut für Neuropathologie, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
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19
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Scardigli M, Pesce L, Brady N, Mazzamuto G, Gavryusev V, Silvestri L, Hof PR, Destrieux C, Costantini I, Pavone FS. Comparison of Different Tissue Clearing Methods for Three-Dimensional Reconstruction of Human Brain Cellular Anatomy Using Advanced Imaging Techniques. Front Neuroanat 2021; 15:752234. [PMID: 34867215 PMCID: PMC8632656 DOI: 10.3389/fnana.2021.752234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/13/2021] [Indexed: 01/29/2023] Open
Abstract
The combination of tissue clearing techniques with advanced optical microscopy facilitates the achievement of three-dimensional (3D) reconstruction of macroscopic specimens at high resolution. Whole mouse organs or even bodies have been analyzed, while the reconstruction of the human nervous system remains a challenge. Although several tissue protocols have been proposed, the high autofluorescence and variable post-mortem conditions of human specimens negatively affect the quality of the images in terms of achievable transparency and staining contrast. Moreover, homogeneous staining of high-density epitopes, such as neuronal nuclear antigen (NeuN), creates an additional challenge. Here, we evaluated different tissue transformation approaches to find the best solution to uniformly clear and label all neurons in the human cerebral cortex using anti-NeuN antibodies in combination with confocal and light-sheet fluorescence microscopy (LSFM). Finally, we performed mesoscopic high-resolution 3D reconstruction of the successfully clarified and stained samples with LSFM.
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Affiliation(s)
- Marina Scardigli
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Luca Pesce
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Niamh Brady
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
- Department of Biology, University of Florence, Florence, Italy
| | - Francesco S. Pavone
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
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20
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Li Y, Walker LA, Zhao Y, Edwards EM, Michki NS, Cheng HPJ, Ghazzi M, Chen TY, Chen M, Roossien DH, Cai D. Bitbow Enables Highly Efficient Neuronal Lineage Tracing and Morphology Reconstruction in Single Drosophila Brains. Front Neural Circuits 2021; 15:732183. [PMID: 34744636 PMCID: PMC8564373 DOI: 10.3389/fncir.2021.732183] [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: 06/28/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022] Open
Abstract
Identifying the cellular origins and mapping the dendritic and axonal arbors of neurons have been century old quests to understand the heterogeneity among these brain cells. Current Brainbow based transgenic animals take the advantage of multispectral labeling to differentiate neighboring cells or lineages, however, their applications are limited by the color capacity. To improve the analysis throughput, we designed Bitbow, a digital format of Brainbow which exponentially expands the color palette to provide tens of thousands of spectrally resolved unique labels. We generated transgenic Bitbow Drosophila lines, established statistical tools, and streamlined sample preparation, image processing, and data analysis pipelines to conveniently mapping neural lineages, studying neuronal morphology and revealing neural network patterns with unprecedented speed, scale, and resolution.
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Affiliation(s)
- Ye Li
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Logan A Walker
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, United States
| | - Yimeng Zhao
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Erica M Edwards
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Nigel S Michki
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, United States
| | - Hon Pong Jimmy Cheng
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Marya Ghazzi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Tiffany Y Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Maggie Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Douglas H Roossien
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Dawen Cai
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States.,Biophysics LS&A, University of Michigan, Ann Arbor, MI, United States.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States
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21
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Endo M, Maruoka H, Okabe S. Advanced Technologies for Local Neural Circuits in the Cerebral Cortex. Front Neuroanat 2021; 15:757499. [PMID: 34803616 PMCID: PMC8595196 DOI: 10.3389/fnana.2021.757499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
The neural network in the brain can be viewed as an integrated system assembled from a large number of local neural circuits specialized for particular brain functions. Activities of neurons in local neural circuits are thought to be organized both spatially and temporally under the rules optimized for their roles in information processing. It is well perceived that different areas of the mammalian neocortex have specific cognitive functions and distinct computational properties. However, the organizational principles of the local neural circuits in different cortical regions have not yet been clarified. Therefore, new research principles and related neuro-technologies that enable efficient and precise recording of large-scale neuronal activities and synaptic connections are necessary. Innovative technologies for structural analysis, including tissue clearing and expansion microscopy, have enabled super resolution imaging of the neural circuits containing thousands of neurons at a single synapse resolution. The imaging resolution and volume achieved by new technologies are beyond the limits of conventional light or electron microscopic methods. Progress in genome editing and related technologies has made it possible to label and manipulate specific cell types and discriminate activities of multiple cell types. These technologies will provide a breakthrough for multiscale analysis of the structure and function of local neural circuits. This review summarizes the basic concepts and practical applications of the emerging technologies and new insight into local neural circuits obtained by these technologies.
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Affiliation(s)
| | | | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
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22
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Abstract
Fluorescence imaging techniques play a pivotal role in our understanding of the nervous system. The emergence of various super-resolution microscopy methods and specialized fluorescent probes enables direct insight into neuronal structure and protein arrangements in cellular subcompartments with so far unmatched resolution. Super-resolving visualization techniques in neurons unveil a novel understanding of cytoskeletal composition, distribution, motility, and signaling of membrane proteins, subsynaptic structure and function, and neuron-glia interaction. Well-defined molecular targets in autoimmune and neurodegenerative disease models provide excellent starting points for in-depth investigation of disease pathophysiology using novel and innovative imaging methodology. Application of super-resolution microscopy in human brain samples and for testing clinical biomarkers is still in its infancy but opens new opportunities for translational research in neurology and neuroscience. In this review, we describe how super-resolving microscopy has improved our understanding of neuronal and brain function and dysfunction in the last two decades.
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Affiliation(s)
- Christian Werner
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Christian Geis
- Section Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
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23
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Five trendy technologies: where are they now? Nature 2021. [DOI: 10.1038/d41586-021-01684-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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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: 9] [Impact Index Per Article: 2.3] [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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Minehart JA, Speer CM. A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. Front Synaptic Neurosci 2021; 12:615059. [PMID: 33469427 PMCID: PMC7813761 DOI: 10.3389/fnsyn.2020.615059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
A key challenge in developmental neuroscience is identifying the local regulatory mechanisms that control neurite and synaptic refinement over large brain volumes. Innovative molecular techniques and high-resolution imaging tools are beginning to reshape our view of how local protein translation in subcellular compartments drives axonal, dendritic, and synaptic development and plasticity. Here we review recent progress in three areas of neurite and synaptic study in situ-compartment-specific transcriptomics/translatomics, targeted proteomics, and super-resolution imaging analysis of synaptic organization and development. We discuss synergies between sequencing and imaging techniques for the discovery and validation of local molecular signaling mechanisms regulating synaptic development, plasticity, and maintenance in circuits.
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Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
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