1
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Shapson-Coe A, Januszewski M, Berger DR, Pope A, Wu Y, Blakely T, Schalek RL, Li PH, Wang S, Maitin-Shepard J, Karlupia N, Dorkenwald S, Sjostedt E, Leavitt L, Lee D, Troidl J, Collman F, Bailey L, Fitzmaurice A, Kar R, Field B, Wu H, Wagner-Carena J, Aley D, Lau J, Lin Z, Wei D, Pfister H, Peleg A, Jain V, Lichtman JW. A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution. Science 2024; 384:eadk4858. [PMID: 38723085 DOI: 10.1126/science.adk4858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 03/27/2024] [Indexed: 05/31/2024]
Abstract
To fully understand how the human brain works, knowledge of its structure at high resolution is needed. Presented here is a computationally intensive reconstruction of the ultrastructure of a cubic millimeter of human temporal cortex that was surgically removed to gain access to an underlying epileptic focus. It contains about 57,000 cells, about 230 millimeters of blood vessels, and about 150 million synapses and comprises 1.4 petabytes. Our analysis showed that glia outnumber neurons 2:1, oligodendrocytes were the most common cell, deep layer excitatory neurons could be classified on the basis of dendritic orientation, and among thousands of weak connections to each neuron, there exist rare powerful axonal inputs of up to 50 synapses. Further studies using this resource may bring valuable insights into the mysteries of the human brain.
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Affiliation(s)
- Alexander Shapson-Coe
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Queen Mary, University of London, London E1 4NS, UK
| | | | - Daniel R Berger
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Art Pope
- Google Research, Mountain View, CA 94043, USA
| | - Yuelong Wu
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | | | - Richard L Schalek
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Peter H Li
- Google Research, Mountain View, CA 94043, USA
| | - Shuohong Wang
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | | | - Neha Karlupia
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Sven Dorkenwald
- Google Research, Mountain View, CA 94043, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08540, USA
- Computer Science Department, Princeton University, Princeton, NJ 08540, USA
| | - Evelina Sjostedt
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | | | - Dongil Lee
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jakob Troidl
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | | | - Luke Bailey
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Angerica Fitzmaurice
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Northeastern University, Boston, MA 02115, USA
| | - Rohin Kar
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Northeastern University, Boston, MA 02115, USA
| | - Benjamin Field
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Northeastern University, Boston, MA 02115, USA
| | - Hank Wu
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Northeastern University, Boston, MA 02115, USA
| | - Julian Wagner-Carena
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - David Aley
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Joanna Lau
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Zudi Lin
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Donglai Wei
- Computer Science Department, Boston College, Chestnut Hill, MA 02467, USA
| | - Hanspeter Pfister
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Adi Peleg
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Google, Cambridge, MA 02142, USA
| | - Viren Jain
- Google Research, Mountain View, CA 94043, USA
| | - Jeff W Lichtman
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
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2
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Riboul DV, Crill S, Oliva CD, Restifo MG, Joseph R, Joseph K, Nguyen KC, Hall DH, Fily Y, Macleod GT. Ultrastructural analysis reveals mitochondrial placement independent of synapse placement in fine caliber C. elegans neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.30.542959. [PMID: 37398149 PMCID: PMC10312582 DOI: 10.1101/2023.05.30.542959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Neurons rely on mitochondria for an efficient supply of ATP and other metabolites. However, while neurons are highly elongated, mitochondria are discrete and limited in number. Due to the slow rates of diffusion over long distances it follows that neurons would benefit from an ability to control the distribution of mitochondria to sites of high metabolic activity, such as synapses. It is assumed that neurons' possess this capacity, but ultrastructural data over substantial portions of a neuron's extent that would allow for tests of such hypotheses are scarce. Here, we mined the Caenorhabditis elegans electron micrographs of John White and Sydney Brenner and found systematic differences in average mitochondrial length (ranging from 1.3 to 2.4 μm), volume density (3.7% to 6.5%) and diameter (0.18 to 0.24 μm) between neurons of different neurotransmitter type and function, but found limited differences in mitochondrial morphometrics between axons and dendrites of the same neurons. Analyses of distance intervals found mitochondria to be distributed randomly with respect to presynaptic specializations, and an indication that mitochondria were displaced from postsynaptic specializations. Presynaptic specializations were primarily localized to varicosities, but mitochondria were no more likely to be found in synaptic varicosities than non-synaptic varicosities. Consistently, mitochondrial volume density was no greater in varicosities with synapses. Therefore, beyond the capacity to disperse mitochondria throughout their length, at least in C. elegans, fine caliber neurons manifest limited sub-cellular control of mitochondrial size and distribution.
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Stein J, Ericsson M, Nofal M, Magni L, Aufmkolk S, McMillan RB, Breimann L, Herlihy CP, Lee SD, Willemin A, Wohlmann J, Arguedas-Jimenez L, Yin P, Pombo A, Church GM, Wu CK. Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.576943. [PMID: 38370628 PMCID: PMC10871237 DOI: 10.1101/2024.02.05.576943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
DNA-PAINT combined with total Internal Reflection Fluorescence (TIRF) microscopy enables the highest localization precisions, down to single nanometers in thin biological samples, due to TIRF's unique method for optical sectioning and attaining high contrast. However, most cellular targets elude the accessible TIRF range close to the cover glass and thus require alternative imaging conditions, affecting resolution and image quality. Here, we address this limitation by applying ultrathin physical cryosectioning in combination with DNA-PAINT. With "tomographic & kinetically-enhanced" DNA-PAINT (tokPAINT), we demonstrate the imaging of nuclear proteins with sub-3 nanometer localization precision, advancing the quantitative study of nuclear organization within fixed cells and mouse tissues at the level of single antibodies. We believe that ultrathin sectioning combined with the versatility and multiplexing capabilities of DNA-PAINT will be a powerful addition to the toolbox of quantitative DNA-based super-resolution microscopy in intracellular structural analyses of proteins, RNA and DNA in situ.
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Affiliation(s)
- Johannes Stein
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maria Ericsson
- Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Michel Nofal
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Lorenzo Magni
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Sarah Aufmkolk
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ryan B. McMillan
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Laura Breimann
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Jens Wohlmann
- Department of Biosciences, University of Oslo, Norway
| | - Laura Arguedas-Jimenez
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Peng Yin
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - George M. Church
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chao-Kng Wu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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Basumatary J, Baro N, Joshi P, Mondal PP. Scanning single molecule localization microscopy (scanSMLM) for super-resolution volume imaging. Commun Biol 2023; 6:1050. [PMID: 37848705 PMCID: PMC10582190 DOI: 10.1038/s42003-023-05364-2] [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: 01/05/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023] Open
Abstract
Over the last decade, single-molecule localization microscopy (SMLM) has developed into a set of powerful techniques that have improved spatial resolution over diffraction-limited microscopy and demonstrated the ability to resolve biological features down to a few tens of nanometers. We introduce a single molecule-based scanning SMLM (scanSMLM) system that enables rapid volume imaging. Along with epi-illumination, the system employs a scanning-based 4f detection for volume imaging. The 4f system comprises a combination of an electrically-tunable lens and high NA detection objective lens. By rapidly changing the aperture (or equivalently the focus) of an electrically-tunable lens (ETL) in a 4f detection system, the selectivity of the axial object plane is achieved, for which the image forms in the image/detector plane. So, in principle, one can scan the object volume by just altering the aperture of ETL. Two schemes were adopted to carry out volume imaging: cyclic scan and conventional scan. The cyclic scheme scans the volume in each scan cycle, whereas plane-wise scanning is performed in the conventional scheme. Hence, the cyclic scan ensures uniform dwell time on each frame during data collection, thereby evenly distributing photobleaching throughout the cell volume. With a minimal change in the system hardware (requiring the addition of an ETL lens and related electronics for step-voltage generation) in the existing SMLM system, volume scanning (along the z-axis) can be achieved. To calibrate and derive critical system parameters, we imaged fluorescent beads embedded in a gel-matrix 3D block as a test sample. Subsequently, scanSMLM is employed to visualize the architecture of actin-filaments and the distribution of Meos-Tom20 molecules on the mitochondrial membrane. The technique is further exploited to understand the clustering of Hemagglutinin (HA) protein single molecules in a transfected cell for studying Influenza-A disease progression. The system, for the first time, enabled 3D visualization of HA distribution that revealed HA cluster formation spanning the entire cell volume, post 24 hrs of transfection. Critical biophysical parameters related to HA clusters (density, the number of HA molecules per cluster, axial span, fraction of clustered molecules, and others) are also determined, giving an unprecedented insight into Influenza-A disease progression at the single-molecule level.
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Affiliation(s)
- Jigmi Basumatary
- Nanobioimaging Laboratory, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Neptune Baro
- Nanobioimaging Laboratory, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Prakash Joshi
- Nanobioimaging Laboratory, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Partha Pratim Mondal
- Nanobioimaging Laboratory, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India.
- Centre for Cryogenic Technology, Indian Institute of Science, Bangalore, 560012, India.
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5
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Choi SB, Vatan T, Alexander TA, Zhang C, Mitchell SM, Speer CM, Nemes P. Microanalytical Mass Spectrometry with Super-Resolution Microscopy Reveals a Proteome Transition During Development of the Brain's Circadian Pacemaker. Anal Chem 2023; 95:15208-15216. [PMID: 37792996 PMCID: PMC10728713 DOI: 10.1021/acs.analchem.3c01987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
During brain development, neuronal proteomes are regulated in part by changes in spontaneous and sensory-driven activity in immature neural circuits. A longstanding model for studying activity-dependent circuit refinement is the developing mouse visual system where the formation of axonal projections from the eyes to the brain is influenced by spontaneous retinal activity prior to the onset of vision and by visual experience after eye-opening. The precise proteomic changes in retinorecipient targets that occur during this developmental transition are unknown. Here, we developed a microanalytical proteomics pipeline using capillary electrophoresis (CE) electrospray ionization (ESI) mass spectrometry (MS) in the discovery setting to quantify developmental changes in the chief circadian pacemaker, the suprachiasmatic nucleus (SCN), before and after the onset of photoreceptor-dependent visual function. Nesting CE-ESI with trapped ion mobility spectrometry time-of-flight (TOF) mass spectrometry (TimsTOF PRO) doubled the number of identified and quantified proteins compared to the TOF-only control on the same analytical platform. From 10 ng of peptide input, corresponding to <∼0.5% of the total local tissue proteome, technical triplicate analyses identified 1894 proteins and quantified 1066 proteins, including many with important canonical functions in axon guidance, synapse function, glial cell maturation, and extracellular matrix refinement. Label-free quantification revealed differential regulation for 166 proteins over development, with enrichment of axon guidance-associated proteins prior to eye-opening and synapse-associated protein enrichment after eye-opening. Super-resolution imaging of select proteins using STochastic Optical Reconstruction Microscopy (STORM) corroborated the MS results and showed that increased presynaptic protein abundance pre/post eye-opening in the SCN reflects a developmental increase in synapse number, but not presynaptic size or extrasynaptic protein expression. This work marks the first development and systematic application of TimsTOF PRO for CE-ESI-based microproteomics and the first integration of microanalytical CE-ESI TimsTOF PRO with volumetric super-resolution STORM imaging to expand the repertoire of technologies supporting analytical neuroscience.
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Affiliation(s)
- Sam B. Choi
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Tarlan Vatan
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | | | - Chenghang Zhang
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | | | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | - Peter Nemes
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
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6
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Park S, Jo Y, Kang M, Hong JH, Ko S, Kim S, Park S, Park HC, Shim SH, Choi W. Label-free adaptive optics single-molecule localization microscopy for whole zebrafish. Nat Commun 2023; 14:4185. [PMID: 37443177 PMCID: PMC10344925 DOI: 10.1038/s41467-023-39896-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Specimen-induced aberration has been a major factor limiting the imaging depth of single-molecule localization microscopy (SMLM). Here, we report the application of label-free wavefront sensing adaptive optics to SMLM for deep-tissue super-resolution imaging. The proposed system measures complex tissue aberrations from intrinsic reflectance rather than fluorescence emission and physically corrects the wavefront distortion more than three-fold stronger than the previous limit. This enables us to resolve sub-diffraction morphologies of cilia and oligodendrocytes in whole zebrafish as well as dendritic spines in thick mouse brain tissues at the depth of up to 102 μm with localization number enhancement by up to 37 times and localization precision comparable to aberration-free samples. The proposed approach can expand the application range of SMLM to whole zebrafish that cause the loss of localization number owing to severe tissue aberrations.
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Affiliation(s)
- Sanghyeon Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Republic of Korea
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Yonghyeon Jo
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Republic of Korea
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Minsu Kang
- Department of Chemistry, Korea University, Seoul, Republic of Korea
| | - Jin Hee Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Republic of Korea
| | - Sangyoon Ko
- Department of Chemistry, Korea University, Seoul, Republic of Korea
| | - Suhyun Kim
- Department of Biomedical Sciences, Korea University, Ansan, Republic of Korea
| | - Sangjun Park
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hae Chul Park
- Department of Biomedical Sciences, Korea University, Ansan, Republic of Korea
| | - Sang-Hee Shim
- Department of Chemistry, Korea University, Seoul, Republic of Korea.
| | - Wonshik Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Republic of Korea.
- Department of Physics, Korea University, Seoul, Republic of Korea.
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7
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Zhang C, Yadav S, Speer CM. The synaptic basis of activity-dependent eye-specific competition. Cell Rep 2023; 42:112085. [PMID: 36753422 PMCID: PMC10404640 DOI: 10.1016/j.celrep.2023.112085] [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: 05/31/2022] [Revised: 12/23/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Binocular vision requires proper developmental wiring of eye-specific inputs to the brain. In the thalamus, axons from the two eyes initially overlap in the dorsal lateral geniculate nucleus and undergo activity-dependent competition to segregate into target domains. Here, we combine eye-specific tract tracing with volumetric super-resolution imaging to measure the nanoscale molecular reorganization of developing retinogeniculate eye-specific synapses in the mouse brain. We show there are eye-specific differences in presynaptic vesicle pool size and vesicle association with the active zone at the earliest stages of retinogeniculate refinement but find no evidence of eye-specific differences in subsynaptic domain number, size, or transsynaptic alignment across development. Genetic disruption of spontaneous retinal activity decreases retinogeniculate synapse density, delays the emergence eye-specific differences in vesicle organization, and disrupts subsynaptic domain maturation. These results suggest that activity-dependent eye-specific presynaptic maturation underlies synaptic competition in the mammalian visual system.
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Affiliation(s)
- Chenghang Zhang
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Swapnil Yadav
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Colenso M Speer
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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8
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Albrecht NE, Jiang D, Akhanov V, Hobson R, Speer CM, Robichaux MA, Samuel MA. Rapid 3D-STORM imaging of diverse molecular targets in tissue. CELL REPORTS METHODS 2022; 2:100253. [PMID: 35880013 PMCID: PMC9308169 DOI: 10.1016/j.crmeth.2022.100253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/22/2022] [Accepted: 06/17/2022] [Indexed: 11/25/2022]
Abstract
Fine-scale molecular architecture is critical for nervous system and other biological functions. Methods to visualize these nanoscale structures would benefit from enhanced accessibility, throughput, and tissue compatibility. Here, we report RAIN-STORM, a rapid and scalable nanoscopic imaging optimization approach that improves three-dimensional visualization for subcellular targets in tissue at depth. RAIN-STORM uses conventional tissue samples and readily available reagents and is suitable for commercial instrumentation. To illustrate the efficacy of RAIN-STORM, we utilized the retina. We show that RAIN-STORM imaging is versatile and provide 3D nanoscopic data for over 20 synapse, neuron, glia, and vasculature targets. Sample preparation is also rapid, with a 1-day turnaround from tissue to image, and parameters are suitable for multiple tissue sources. Finally, we show that this method can be applied to clinical samples to reveal nanoscale features of human cells and synapses. RAIN-STORM thus paves the way for high-throughput studies of nanoscopic targets in tissue.
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Affiliation(s)
- Nicholas E. Albrecht
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Danye Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Viktor Akhanov
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert Hobson
- Bruker Nano Surfaces Division, Salt Lake City, UT 84108, USA
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Michael A. Robichaux
- Departments of Ophthalmology and Biochemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Melanie A. Samuel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
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9
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Vatan T, Minehart JA, Zhang C, Agarwal V, Yang J, Speer CM. Volumetric super-resolution imaging by serial ultrasectioning and stochastic optical reconstruction microscopy in mouse neural tissue. STAR Protoc 2021; 2:100971. [PMID: 34901889 PMCID: PMC8637648 DOI: 10.1016/j.xpro.2021.100971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Here, we present a protocol for collecting large-volume, four-color, single-molecule localization imaging data from neural tissue. We have applied this technique to map the location and identities of chemical synapses across whole cells in mouse retinae. Our sample preparation approach improves 3D STORM image quality by reducing tissue scattering, photobleaching, and optical distortions associated with deep imaging. This approach can be extended for use on other tissue types enabling life scientists to perform volumetric super-resolution imaging in diverse biological models. For complete details on the use and execution of this protocol, please refer to Sigal et al. (2015).
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Affiliation(s)
- Tarlan Vatan
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Neuroscience and Cognitive Science Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Jacqueline A. Minehart
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Neuroscience and Cognitive Science Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Chenghang Zhang
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Vatsal Agarwal
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Jerry Yang
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Brain and Behavior Institute, University of Maryland, College Park, MD 20742, USA
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10
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Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [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: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
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Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
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11
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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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12
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Lyu X, Wang J, Wang J, Yin YS, Zhu Y, Li LL, Huang S, Peng S, Xue B, Liao R, Wang SQ, Long M, Wohland T, Chua BT, Sun Y, Li P, Chen XW, Xu L, Chen FJ, Li P. A gel-like condensation of Cidec generates lipid-permeable plates for lipid droplet fusion. Dev Cell 2021; 56:2592-2606.e7. [PMID: 34508658 DOI: 10.1016/j.devcel.2021.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 05/02/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Membrane contact between intracellular organelles is important in mediating organelle communication. However, the assembly of molecular machinery at membrane contact site and its internal organization correlating with its functional activity remain unclear. Here, we demonstrate that a gel-like condensation of Cidec, a crucial protein for obesity development by facilitating lipid droplet (LD) fusion, occurs at the LD-LD contact site (LDCS) through phase separation. The homomeric interaction between the multivalent N terminus of Cidec is sufficient to promote its phase separation both in vivo and in vitro. Interestingly, Cidec condensation at LDCSs generates highly plastic and lipid-permeable fusion plates that are geometrically constrained by donor LDs. In addition, Cidec condensates are distributed unevenly in the fusion plate generating stochastic sub-compartments that may represent unique lipid passageways during LD fusion. We have thus uncovered the organization and functional significance of geometry-constrained Cidec phase separation in mediating LD fusion and lipid homeostasis.
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Affiliation(s)
- Xuchao Lyu
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianqin Wang
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ye-Sheng Yin
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yun Zhu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Lin-Lin Li
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Shuangru Huang
- Departments of Biological Sciences and Chemistry and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Shuang Peng
- Institute of Mechanics, Chinese Academy of Sciences, No.15 Beisihuanxi Road, Beijing 100190, China
| | - Boxin Xue
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Rongyu Liao
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shi-Qiang Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Mian Long
- Institute of Mechanics, Chinese Academy of Sciences, No.15 Beisihuanxi Road, Beijing 100190, China
| | - Thorsten Wohland
- Departments of Biological Sciences and Chemistry and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Boon Tin Chua
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yujie Sun
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiao-Wei Chen
- State Key Laboratory of Membrane Biology, Center for Life Sciences and Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100101, China
| | - Li Xu
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Shanghai Qi Zhi Institute, Shanghai 200030, China
| | - Feng-Jung Chen
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Shanghai Qi Zhi Institute, Shanghai 200030, China.
| | - Peng Li
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Shanghai Qi Zhi Institute, Shanghai 200030, China.
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13
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Pottackal J, Singer JH, Demb JB. Computational and Molecular Properties of Starburst Amacrine Cell Synapses Differ With Postsynaptic Cell Type. Front Cell Neurosci 2021; 15:660773. [PMID: 34381333 PMCID: PMC8351878 DOI: 10.3389/fncel.2021.660773] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/08/2021] [Indexed: 11/22/2022] Open
Abstract
A presynaptic neuron can increase its computational capacity by transmitting functionally distinct signals to each of its postsynaptic cell types. To determine whether such computational specialization occurs over fine spatial scales within a neurite arbor, we investigated computation at output synapses of the starburst amacrine cell (SAC), a critical component of the classical direction-selective (DS) circuit in the retina. The SAC is a non-spiking interneuron that co-releases GABA and acetylcholine and forms closely spaced (<5 μm) inhibitory synapses onto two postsynaptic cell types: DS ganglion cells (DSGCs) and neighboring SACs. During dynamic optogenetic stimulation of SACs in mouse retina, whole-cell recordings of inhibitory postsynaptic currents revealed that GABAergic synapses onto DSGCs exhibit stronger low-pass filtering than those onto neighboring SACs. Computational analyses suggest that this filtering difference can be explained primarily by presynaptic properties, rather than those of the postsynaptic cells per se. Consistent with functionally diverse SAC presynapses, blockade of N-type voltage-gated calcium channels abolished GABAergic currents in SACs but only moderately reduced GABAergic and cholinergic currents in DSGCs. These results jointly demonstrate how specialization of synaptic outputs could enhance parallel processing in a compact interneuron over fine spatial scales. Moreover, the distinct transmission kinetics of GABAergic SAC synapses are poised to support the functional diversity of inhibition within DS circuitry.
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Affiliation(s)
- Joseph Pottackal
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, United States.,Department of Biology, University of Maryland, College Park, College Park, MD, United States
| | - Joshua H Singer
- Department of Biology, University of Maryland, College Park, College Park, MD, United States
| | - Jonathan B Demb
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, United States.,Department of Ophthalmology and Visual Science, Yale University, New Haven, CT, United States.,Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, United States.,Department of Neuroscience, Yale University, New Haven, CT, United States
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14
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Shih CT, Chen NY, Wang TY, He GW, Wang GT, Lin YJ, Lee TK, Chiang AS. NeuroRetriever: Automatic Neuron Segmentation for Connectome Assembly. Front Syst Neurosci 2021; 15:687182. [PMID: 34366800 PMCID: PMC8342815 DOI: 10.3389/fnsys.2021.687182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/21/2021] [Indexed: 11/15/2022] Open
Abstract
Segmenting individual neurons from a large number of noisy raw images is the first step in building a comprehensive map of neuron-to-neuron connections for predicting information flow in the brain. Thousands of fluorescence-labeled brain neurons have been imaged. However, mapping a complete connectome remains challenging because imaged neurons are often entangled and manual segmentation of a large population of single neurons is laborious and prone to bias. In this study, we report an automatic algorithm, NeuroRetriever, for unbiased large-scale segmentation of confocal fluorescence images of single neurons in the adult Drosophila brain. NeuroRetriever uses a high-dynamic-range thresholding method to segment three-dimensional morphology of single neurons based on branch-specific structural features. Applying NeuroRetriever to automatically segment single neurons in 22,037 raw brain images, we successfully retrieved 28,125 individual neurons validated by human segmentation. Thus, automated NeuroRetriever will greatly accelerate 3D reconstruction of the single neurons for constructing the complete connectomes.
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Affiliation(s)
- Chi-Tin Shih
- Department of Applied Physics, Tunghai University, Taichung, Taiwan.,Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Nan-Yow Chen
- National Center for High-Performance Computing, National Applied Research Laboratories, Hsinchu, Taiwan
| | - Ting-Yuan Wang
- Institute of Biotechnology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Guan-Wei He
- Department of Computer Science, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Guo-Tzau Wang
- National Center for High-Performance Computing, National Applied Research Laboratories, Hsinchu, Taiwan
| | - Yen-Jen Lin
- National Center for High-Performance Computing, National Applied Research Laboratories, Hsinchu, Taiwan
| | - Ting-Kuo Lee
- Institute of Physics, Academia Sinica, Taipei, Taiwan.,Department of Physics, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ann-Shyn Chiang
- Department of Applied Physics, Tunghai University, Taichung, Taiwan.,Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan.,Institute of Physics, Academia Sinica, Taipei, Taiwan.,Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.,Kavli Institute for Brain and Mind, University of California, San Diego, San Diego, CA, United States
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15
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Tkatchenko TV, Tkatchenko AV. Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection. BMC Med Genomics 2021; 14:153. [PMID: 34107987 PMCID: PMC8190860 DOI: 10.1186/s12920-021-01005-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Refractive eye development is regulated by optical defocus in a process of emmetropization. Excessive exposure to negative optical defocus often leads to the development of myopia. However, it is still largely unknown how optical defocus is detected by the retina. METHODS Here, we used genome-wide RNA-sequencing to conduct analysis of the retinal gene expression network underlying contrast perception and refractive eye development. RESULTS We report that the genetic network subserving contrast perception plays an important role in optical defocus detection and emmetropization. Our results demonstrate an interaction between contrast perception, the retinal circadian clock pathway and the signaling pathway underlying optical defocus detection. We also observe that the relative majority of genes causing human myopia are involved in the processing of optical defocus. CONCLUSIONS Together, our results support the hypothesis that optical defocus is perceived by the retina using contrast as a proxy and provide new insights into molecular signaling underlying refractive eye development.
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Affiliation(s)
| | - Andrei V. Tkatchenko
- Department of Ophthalmology, Columbia University, New York, NY USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY USA
- Edward S. Harkness Eye Institute, Research Annex Room 415, 635 W. 165th Street, New York, NY 10032 USA
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16
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Choquet D, Sainlos M, Sibarita JB. Advanced imaging and labelling methods to decipher brain cell organization and function. Nat Rev Neurosci 2021; 22:237-255. [PMID: 33712727 DOI: 10.1038/s41583-021-00441-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2021] [Indexed: 01/31/2023]
Abstract
The brain is arguably the most complex organ. The branched and extended morphology of nerve cells, their subcellular complexity, the multiplicity of brain cell types as well as their intricate connectivity and the scattering properties of brain tissue present formidable challenges to the understanding of brain function. Neuroscientists have often been at the forefront of technological and methodological developments to overcome these hurdles to visualize, quantify and modify cell and network properties. Over the last few decades, the development of advanced imaging methods has revolutionized our approach to explore the brain. Super-resolution microscopy and tissue imaging approaches have recently exploded. These instrumentation-based innovations have occurred in parallel with the development of new molecular approaches to label protein targets, to evolve new biosensors and to target them to appropriate cell types or subcellular compartments. We review the latest developments for labelling and functionalizing proteins with small localization and functionalized reporters. We present how these molecular tools are combined with the development of a wide variety of imaging methods that break either the diffraction barrier or the tissue penetration depth limits. We put these developments in perspective to emphasize how they will enable step changes in our understanding of the brain.
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Affiliation(s)
- Daniel Choquet
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France. .,University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4, Bordeaux, France.
| | - Matthieu Sainlos
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.
| | - Jean-Baptiste Sibarita
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.
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17
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Dankovich TM, Rizzoli SO. Challenges facing quantitative large-scale optical super-resolution, and some simple solutions. iScience 2021; 24:102134. [PMID: 33665555 PMCID: PMC7898072 DOI: 10.1016/j.isci.2021.102134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Optical super-resolution microscopy (SRM) has enabled biologists to visualize cellular structures with near-molecular resolution, giving unprecedented access to details about the amounts, sizes, and spatial distributions of macromolecules in the cell. Precisely quantifying these molecular details requires large datasets of high-quality, reproducible SRM images. In this review, we discuss the unique set of challenges facing quantitative SRM, giving particular attention to the shortcomings of conventional specimen preparation techniques and the necessity for optimal labeling of molecular targets. We further discuss the obstacles to scaling SRM methods, such as lengthy image acquisition and complex SRM data analysis. For each of these challenges, we review the recent advances in the field that circumvent these pitfalls and provide practical advice to biologists for optimizing SRM experiments.
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Affiliation(s)
- Tal M. Dankovich
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, Göttingen 37073, Germany
- International Max Planck Research School for Neuroscience, Göttingen, Germany
| | - Silvio O. Rizzoli
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, Göttingen 37073, Germany
- Biostructural Imaging of Neurodegeneration (BIN) Center & Multiscale Bioimaging Excellence Center, Göttingen 37075, Germany
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18
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Okabe S. Recent advances in computational methods for measurement of dendritic spines imaged by light microscopy. Microscopy (Oxf) 2021; 69:196-213. [PMID: 32244257 DOI: 10.1093/jmicro/dfaa016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 02/04/2020] [Accepted: 03/23/2020] [Indexed: 12/13/2022] Open
Abstract
Dendritic spines are small protrusions that receive most of the excitatory inputs to the pyramidal neurons in the neocortex and the hippocampus. Excitatory neural circuits in the neocortex and hippocampus are important for experience-dependent changes in brain functions, including postnatal sensory refinement and memory formation. Several lines of evidence indicate that synaptic efficacy is correlated with spine size and structure. Hence, precise and accurate measurement of spine morphology is important for evaluation of neural circuit function and plasticity. Recent advances in light microscopy and image analysis techniques have opened the way toward a full description of spine nanostructure. In addition, large datasets of spine nanostructure can be effectively analyzed using machine learning techniques and other mathematical approaches, and recent advances in super-resolution imaging allow researchers to analyze spine structure at an unprecedented level of precision. This review summarizes computational methods that can effectively identify, segment and quantitate dendritic spines in either 2D or 3D imaging. Nanoscale analysis of spine structure and dynamics, combined with new mathematical approaches, will facilitate our understanding of spine functions in physiological and pathological conditions.
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Affiliation(s)
- Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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19
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Codron P, Letournel F, Marty S, Renaud L, Bodin A, Duchesne M, Verny C, Lenaers G, Duyckaerts C, Julien J, Cassereau J, Chevrollier A. STochastic Optical Reconstruction Microscopy (STORM) reveals the nanoscale organization of pathological aggregates in human brain. Neuropathol Appl Neurobiol 2021; 47:127-142. [PMID: 32688444 PMCID: PMC7891317 DOI: 10.1111/nan.12646] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/12/2020] [Accepted: 07/12/2020] [Indexed: 12/31/2022]
Abstract
AIMS Histological analysis of brain tissue samples provides valuable information about the pathological processes leading to common neurodegenerative disorders. In this context, the development of novel high-resolution imaging approaches is a current challenge in neuroscience. METHODS To this end, we used a recent super-resolution imaging technique called STochastic Optical Reconstruction Microscopy (STORM) to analyse human brain sections. We combined STORM cell imaging protocols with neuropathological techniques to image cryopreserved brain samples from control subjects and patients with neurodegenerative diseases. RESULTS This approach allowed us to perform 2D-, 3D- and two-colour-STORM in neocortex, white matter and brainstem samples. STORM proved to be particularly effective at visualizing the organization of dense protein inclusions and we imaged with a <50 nm resolution pathological aggregates within the central nervous system of patients with Alzheimer's disease, Parkinson's disease, Lewy body dementia and fronto-temporal lobar degeneration. Aggregated Aβ branches appeared reticulated and cross-linked in the extracellular matrix, with widths from 60 to 240 nm. Intraneuronal Tau and TDP-43 inclusions were denser, with a honeycomb pattern in the soma and a filamentous organization in the axons. Finally, STORM imaging of α-synuclein pathology revealed the internal organization of Lewy bodies that could not be observed by conventional fluorescence microscopy. CONCLUSIONS STORM imaging of human brain samples opens further gates to a more comprehensive understanding of common neurological disorders. The convenience of this technique should open a straightforward extension of its application for super-resolution imaging of the human brain, with promising avenues to current challenges in neuroscience.
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Affiliation(s)
- P. Codron
- Service de NeurologieCentre Hospitalier Universitaire d’AngersAngersFrance
- Laboratoire de Neurobiologie et NeuropathologieCentre Hospitalier Universitaire d’AngersAngersFrance
- Équipe MitolabInstitut MITOVASCINSERM U1083CNRS 6015Université d'AngersAngersFrance
| | - F. Letournel
- Service de NeurologieCentre Hospitalier Universitaire d’AngersAngersFrance
- Laboratoire de Neurobiologie et NeuropathologieCentre Hospitalier Universitaire d’AngersAngersFrance
| | - S. Marty
- Institut du Cerveau et de la Moelle épinièreINSERM U1127CNRS UMR7225Sorbonne UniversitéParisFrance
| | - L. Renaud
- CERVO Brain Research Centre2601 Chemin de la CanardièreQuébecQCCanada
| | - A. Bodin
- Équipe MitolabInstitut MITOVASCINSERM U1083CNRS 6015Université d'AngersAngersFrance
| | - M. Duchesne
- Laboratoire d'Anatomie PathologiqueCentre Hospitalier Universitaire DupuytrenLimogesFrance
- Centre de Référence des Neuropathies Périphériques RaresCentre Hospitalier Universitaire DupuytrenLimogesFrance
| | - C. Verny
- Service de NeurologieCentre Hospitalier Universitaire d’AngersAngersFrance
- Équipe MitolabInstitut MITOVASCINSERM U1083CNRS 6015Université d'AngersAngersFrance
| | - G. Lenaers
- Équipe MitolabInstitut MITOVASCINSERM U1083CNRS 6015Université d'AngersAngersFrance
| | - C. Duyckaerts
- Institut du Cerveau et de la Moelle épinièreINSERM U1127CNRS UMR7225Sorbonne UniversitéParisFrance
| | - J.‐P. Julien
- CERVO Brain Research Centre2601 Chemin de la CanardièreQuébecQCCanada
- Department of Psychiatry and NeuroscienceLaval UniversityQuébecQCCanada
| | - J. Cassereau
- Service de NeurologieCentre Hospitalier Universitaire d’AngersAngersFrance
- Équipe MitolabInstitut MITOVASCINSERM U1083CNRS 6015Université d'AngersAngersFrance
| | - A. Chevrollier
- Équipe MitolabInstitut MITOVASCINSERM U1083CNRS 6015Université d'AngersAngersFrance
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20
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Imaging of spine synapses using super-resolution microscopy. Anat Sci Int 2021; 96:343-358. [PMID: 33459976 DOI: 10.1007/s12565-021-00603-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
Neuronal circuits in the neocortex and hippocampus are essential for higher brain functions such as motor learning and spatial memory. In the mammalian forebrain, most excitatory synapses of pyramidal neurons are formed on spines, which are tiny protrusions extending from the dendritic shaft. The spine contains specialized molecular machinery that regulates synaptic transmission and plasticity. Spine size correlates with the efficacy of synaptic transmission, and spine morphology affects signal transduction at the post-synaptic compartment. Plasticity-related changes in the structural and molecular organization of spine synapses are thought to underlie the cellular basis of learning and memory. Recent advances in super-resolution microscopy have revealed the molecular mechanisms of the nanoscale synaptic structures regulating synaptic transmission and plasticity in living neurons, which are difficult to investigate using electron microscopy alone. In this review, we summarize recent advances in super-resolution imaging of spine synapses and discuss the implications of nanoscale structures in the regulation of synaptic function, learning, and memory.
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21
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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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22
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Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J, Manley S, Jungmann R, Sauer M, Lakadamyali M, Zimmer C. Single-molecule localization microscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:39. [PMID: 35663461 PMCID: PMC9160414 DOI: 10.1038/s43586-021-00038-x] [Citation(s) in RCA: 279] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM.
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Affiliation(s)
- Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
| | - Melina T. Gyparaki
- Department of Biology, University of Pennsylvania,
Philadelphia, PA, USA
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
- ;
;
;
;
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
- ;
;
;
;
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
- ;
;
;
;
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- ;
;
;
;
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
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23
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Famiglietti EV. Morphological identification and systematic classification of mammalian retinal ganglion cells. I. Rabbit retinal ganglion cells. J Comp Neurol 2020; 528:3305-3450. [PMID: 32725618 DOI: 10.1002/cne.24998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 11/10/2022]
Abstract
Retinal ganglion cells (RGCs) convey visual signals to 50 regions of the brain. For reasons of interest and convenience, they constitute an excellent system for the study of brain structure and function. There is general agreement that, absent a complete "parts list," understanding how the nervous system processes information will remain an elusive goal. Recent studies indicate that there are 30-50 types of ganglion cell in mouse retina, whereas only a few years ago it was still written that mice and the more visually oriented lagomorphs had less than 20 types of RGC. More than 30 years ago, I estimated that rabbits have about 40 types of RGC. The present study indicates that this number is much too low. I have employed the old but powerful method of Golgi-impregnation to rabbit retina, studying the range of component neurons in this already well-studied retinal system. Close quantitative and qualitative analyses of 1,142 RGCs in 26 retinas take into account cell body and dendritic field size, level(s) of dendritic stratification in the retina's inner plexiform layer, and details of dendritic branching. Ninety-one morphologies are recognized. Of these, at least 32 can be correlated with physiologically studied RGCs, dye-injected for morphological analysis. It is unlikely that rabbits have 91 types of RGC, but is argued here that this number lies between 60 and 70. The present study provides a "yardstick" for measuring the output of future molecular studies that may be more definitive in fixing the number of RGC types in rabbit retina.
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Affiliation(s)
- Edward V Famiglietti
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island, USA.,Division of Ophthalmology, Rhode Island Hospital, Providence, Rhode Island, USA
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24
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Li M, Huang ZL. Rethinking resolution estimation in fluorescence microscopy: from theoretical resolution criteria to super-resolution microscopy. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1776-1785. [PMID: 33351176 DOI: 10.1007/s11427-020-1785-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 10/20/2020] [Indexed: 11/28/2022]
Abstract
Resolution is undoubtedly the most important parameter in optical microscopy by providing an estimation on the maximum resolving power of a certain optical microscope. For centuries, the resolution of an optical microscope is generally considered to be limited only by the numerical aperture of the optical system and the wavelength of light. However, since the invention and popularity of various advanced fluorescence microscopy techniques, especially super-resolution fluorescence microscopy, many new methods have been proposed for estimating the resolution, leading to confusions for researchers who need to quantify the resolution of their fluorescence microscopes. In this paper, we firstly summarize the early concepts and criteria for predicting the resolution limit of an ideal optical system. Then, we discuss some important influence factors that deteriorate the resolution of a certain fluorescence microscope. Finally, we provide methods and examples on how to measure the resolution of a fluorescence microscope from captured fluorescence images. This paper aims to answer as best as possible the theoretical and practical issues regarding the resolution estimation in fluorescence microscopy.
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Affiliation(s)
- Mengting Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhen-Li Huang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China. .,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, China. .,School of Biomedical Engineering, Hainan University, Haikou, 570228, China.
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25
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Zhang K, Sun Y, Wu S, Zhou M, Zhang X, Zhou R, Zhang T, Gao Y, Chen T, Chen Y, Yao X, Watanabe Y, Tian M, Zhang H. Systematic imaging in medicine: a comprehensive review. Eur J Nucl Med Mol Imaging 2020; 48:1736-1758. [PMID: 33210241 DOI: 10.1007/s00259-020-05107-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/08/2020] [Indexed: 01/05/2023]
Abstract
Systematic imaging can be broadly defined as the systematic identification and characterization of biological processes at multiple scales and levels. In contrast to "classical" diagnostic imaging, systematic imaging emphasizes on detecting the overall abnormalities including molecular, functional, and structural alterations occurring during disease course in a systematic manner, rather than just one aspect in a partial manner. Concomitant efforts including improvement of imaging instruments, development of novel imaging agents, and advancement of artificial intelligence are warranted for achievement of systematic imaging. It is undeniable that scientists and radiologists will play a predominant role in directing this burgeoning field. This article introduces several recent developments in imaging modalities and nanoparticles-based imaging agents, and discusses how systematic imaging can be achieved. In the near future, systematic imaging which combines multiple imaging modalities with multimodal imaging agents will pave a new avenue for comprehensive characterization of diseases, successful achievement of image-guided therapy, precise evaluation of therapeutic effects, and rapid development of novel pharmaceuticals, with the final goal of improving human health-related outcomes.
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Affiliation(s)
- Kai Zhang
- Department of Nuclear Medicine and PET center, The Second Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China.,Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center, School of Life Sciences, Peking University, Beijing, China
| | - Shuang Wu
- Department of Nuclear Medicine and PET center, The Second Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China
| | - Min Zhou
- Department of Nuclear Medicine and PET center, The Second Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China.,Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohui Zhang
- Department of Nuclear Medicine and PET center, The Second Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China
| | - Rui Zhou
- Department of Nuclear Medicine and PET center, The Second Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China
| | - Tingting Zhang
- Department of Nuclear Medicine and PET center, The Second Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China
| | - Yuanxue Gao
- Department of Nuclear Medicine and PET center, The Second Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China
| | - Ting Chen
- Department of Nuclear Medicine and PET center, The Second Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China
| | - Yao Chen
- Department of Nuclear Medicine and PET center, The Second Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China
| | - Xin Yao
- Department of Gastroenterology, The First Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yasuyoshi Watanabe
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Mei Tian
- Department of Nuclear Medicine and PET center, The Second Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China.
| | - Hong Zhang
- Department of Nuclear Medicine and PET center, The Second Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China. .,Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, China. .,The College of Biomedical Engineering and Instrument Science of Zhejiang University, Hangzhou, China.
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26
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Fendl S, Vieira RM, Borst A. Conditional protein tagging methods reveal highly specific subcellular distribution of ion channels in motion-sensing neurons. eLife 2020; 9:62953. [PMID: 33079061 PMCID: PMC7655108 DOI: 10.7554/elife.62953] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/14/2020] [Indexed: 11/25/2022] Open
Abstract
Neurotransmitter receptors and ion channels shape the biophysical properties of neurons, from the sign of the response mediated by neurotransmitter receptors to the dynamics shaped by voltage-gated ion channels. Therefore, knowing the localizations and types of receptors and channels present in neurons is fundamental to our understanding of neural computation. Here, we developed two approaches to visualize the subcellular localization of specific proteins in Drosophila: The flippase-dependent expression of GFP-tagged receptor subunits in single neurons and ‘FlpTag’, a versatile new tool for the conditional labelling of endogenous proteins. Using these methods, we investigated the subcellular distribution of the receptors GluClα, Rdl, and Dα7 and the ion channels para and Ih in motion-sensing T4/T5 neurons of the Drosophila visual system. We discovered a strictly segregated subcellular distribution of these proteins and a sequential spatial arrangement of glutamate, acetylcholine, and GABA receptors along the dendrite that matched the previously reported EM-reconstructed synapse distributions.
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Affiliation(s)
- Sandra Fendl
- Max Planck Institute of Neurobiology, Martinsried, Germany.,Graduate School of Systemic Neurosciences, LMU Munich, Martinsried, Germany
| | | | - Alexander Borst
- Max Planck Institute of Neurobiology, Martinsried, Germany.,Graduate School of Systemic Neurosciences, LMU Munich, Martinsried, Germany
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27
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Shen FY, Harrington MM, Walker LA, Cheng HPJ, Boyden ES, Cai D. Light microscopy based approach for mapping connectivity with molecular specificity. Nat Commun 2020; 11:4632. [PMID: 32934230 PMCID: PMC7493953 DOI: 10.1038/s41467-020-18422-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/21/2020] [Indexed: 11/28/2022] Open
Abstract
Mapping neuroanatomy is a foundational goal towards understanding brain function. Electron microscopy (EM) has been the gold standard for connectivity analysis because nanoscale resolution is necessary to unambiguously resolve synapses. However, molecular information that specifies cell types is often lost in EM reconstructions. To address this, we devise a light microscopy approach for connectivity analysis of defined cell types called spectral connectomics. We combine multicolor labeling (Brainbow) of neurons with multi-round immunostaining Expansion Microscopy (miriEx) to simultaneously interrogate morphology, molecular markers, and connectivity in the same brain section. We apply this strategy to directly link inhibitory neuron cell types with their morphologies. Furthermore, we show that correlative Brainbow and endogenous synaptic machinery immunostaining can define putative synaptic connections between neurons, as well as map putative inhibitory and excitatory inputs. We envision that spectral connectomics can be applied routinely in neurobiology labs to gain insights into normal and pathophysiological neuroanatomy.
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Affiliation(s)
- Fred Y Shen
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Margaret M Harrington
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Logan A Walker
- LS & A, Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Hon Pong Jimmy Cheng
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Edward S Boyden
- McGovern Institute, Koch Institute, Department of Media Arts and Sciences, Department of Biological Engineering, and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Dawen Cai
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA.
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
- LS & A, Program in Biophysics, University of Michigan, Ann Arbor, MI, USA.
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28
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Xu J, Ma H, Ma H, Jiang W, Mela CA, Duan M, Zhao S, Gao C, Hahm ER, Lardo SM, Troy K, Sun M, Pai R, Stolz DB, Zhang L, Singh S, Brand RE, Hartman DJ, Hu J, Hainer SJ, Liu Y. Super-resolution imaging reveals the evolution of higher-order chromatin folding in early carcinogenesis. Nat Commun 2020; 11:1899. [PMID: 32313005 PMCID: PMC7171144 DOI: 10.1038/s41467-020-15718-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 03/26/2020] [Indexed: 12/24/2022] Open
Abstract
Genomic DNA is folded into a higher-order structure that regulates transcription and maintains genomic stability. Although progress has been made on understanding biochemical characteristics of epigenetic modifications in cancer, the in-situ higher-order folding of chromatin structure during malignant transformation remains largely unknown. Here, using optimized stochastic optical reconstruction microscopy (STORM) for pathological tissue (PathSTORM), we uncover a gradual decompaction and fragmentation of higher-order chromatin folding throughout all stages of carcinogenesis in multiple tumor types, and prior to tumor formation. Our integrated imaging, genomic, and transcriptomic analyses reveal functional consequences in enhanced transcription activities and impaired genomic stability. We also demonstrate the potential of imaging higher-order chromatin disruption to detect high-risk precursors that cannot be distinguished by conventional pathology. Taken together, our findings reveal gradual decompaction and fragmentation of higher-order chromatin structure as an enabling characteristic in early carcinogenesis to facilitate malignant transformation, which may improve cancer diagnosis, risk stratification, and prevention.
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Affiliation(s)
- Jianquan Xu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Hongqiang Ma
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Hongbin Ma
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China.,Dalian Jinzhou First People's Hospital, Dalian, China
| | - Wei Jiang
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of Pathology, West China Second University Hospital, Sichuan University, 610041, Chengdu, China
| | - Christopher A Mela
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Meihan Duan
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, 100084, Beijing, China
| | - Shimei Zhao
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of Pathology, School of Medicine, Guangxi University of Science and Technology, Guangxi, China
| | - Chenxi Gao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Eun-Ryeong Hahm
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Santana M Lardo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Kris Troy
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Ming Sun
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Reet Pai
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Donna B Stolz
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Lin Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Shivendra Singh
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Randall E Brand
- University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, 15232, USA.,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Douglas J Hartman
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Jing Hu
- University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, 15232, USA.,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15213, USA. .,University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, 15232, USA. .,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
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29
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Whole-Neuron Synaptic Mapping Reveals Spatially Precise Excitatory/Inhibitory Balance Limiting Dendritic and Somatic Spiking. Neuron 2020; 106:566-578.e8. [PMID: 32169170 DOI: 10.1016/j.neuron.2020.02.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/19/2019] [Accepted: 02/11/2020] [Indexed: 02/02/2023]
Abstract
The balance between excitatory and inhibitory (E and I) synapses is thought to be critical for information processing in neural circuits. However, little is known about the spatial principles of E and I synaptic organization across the entire dendritic tree of mammalian neurons. We developed a new open-source reconstruction platform for mapping the size and spatial distribution of E and I synapses received by individual genetically-labeled layer 2/3 (L2/3) cortical pyramidal neurons (PNs) in vivo. We mapped over 90,000 E and I synapses across twelve L2/3 PNs and uncovered structured organization of E and I synapses across dendritic domains as well as within individual dendritic segments. Despite significant domain-specific variation in the absolute density of E and I synapses, their ratio is strikingly balanced locally across dendritic segments. Computational modeling indicates that this spatially precise E/I balance dampens dendritic voltage fluctuations and strongly impacts neuronal firing output.
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30
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Jain V, Murphy-Baum BL, deRosenroll G, Sethuramanujam S, Delsey M, Delaney KR, Awatramani GB. The functional organization of excitation and inhibition in the dendrites of mouse direction-selective ganglion cells. eLife 2020; 9:52949. [PMID: 32096758 PMCID: PMC7069718 DOI: 10.7554/elife.52949] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Recent studies indicate that the precise timing and location of excitation and inhibition (E/I) within active dendritic trees can significantly impact neuronal function. How synaptic inputs are functionally organized at the subcellular level in intact circuits remains unclear. To address this issue, we took advantage of the retinal direction-selective ganglion cell circuit, where directionally tuned inhibition is known to shape non-directional excitatory signals. We combined two-photon calcium imaging with genetic, pharmacological, and single-cell ablation methods to examine the extent to which inhibition ‘vetoes’ excitation at the level of individual dendrites of direction-selective ganglion cells. We demonstrate that inhibition shapes direction selectivity independently within small dendritic segments (<10µm) with remarkable accuracy. The data suggest that the parallel processing schemes proposed for direction encoding could be more fine-grained than previously envisioned.
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Affiliation(s)
- Varsha Jain
- Department of Biology, University of Victoria, Victoria, Canada
| | | | | | | | - Mike Delsey
- Department of Biology, University of Victoria, Victoria, Canada
| | - Kerry R Delaney
- Department of Biology, University of Victoria, Victoria, Canada
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31
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Babcock HP, Huang F, Speer CM. Correcting Artifacts in Single Molecule Localization Microscopy Analysis Arising from Pixel Quantum Efficiency Differences in sCMOS Cameras. Sci Rep 2019; 9:18058. [PMID: 31792238 PMCID: PMC6889274 DOI: 10.1038/s41598-019-53698-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023] Open
Abstract
Optimal analysis of single molecule localization microscopy (SMLM) data acquired with a scientific Complementary Metal-Oxide-Semiconductor (sCMOS) camera relies on statistical compensation for its pixel-dependent gain, offset and readout noise. In this work we show that it is also necessary to compensate for differences in the relative quantum efficiency (RQE) of each pixel. We found differences in RQE on the order of 4% in our tested sCMOS sensors. These differences were large enough to have a noticeable effect on analysis algorithm results, as seen both in simulations and biological imaging data. We discuss how the RQE differences manifest themselves in the analysis results and present the modifications to the Poisson maximum likelihood estimation (MLE) sCMOS analysis algorithm that are needed to correct for the RQE differences.
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Affiliation(s)
- Hazen P Babcock
- Center for Advanced Imaging, Harvard University, Cambridge, MA, 02138, USA.
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Colenso M Speer
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
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32
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Defining the layers of a sensory cilium with STORM and cryoelectron nanoscopy. Proc Natl Acad Sci U S A 2019; 116:23562-23572. [PMID: 31690665 DOI: 10.1073/pnas.1902003116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Primary cilia carry out numerous signaling and sensory functions, and defects in them, "ciliopathies," cause a range of symptoms, including blindness. Understanding of their nanometer-scale ciliary substructures and their disruptions in ciliopathies has been hindered by limitations of conventional microscopic techniques. We have combined cryoelectron tomography, enhanced by subtomogram averaging, with superresolution stochastic optical reconstruction microscopy (STORM) to define subdomains within the light-sensing rod sensory cilium of mouse retinas and reveal previously unknown substructures formed by resident proteins. Domains are demarcated by structural features such as the axoneme and its connections to the ciliary membrane, and are correlated with molecular markers of subcompartments, including the lumen and walls of the axoneme, the membrane glycocalyx, and the intervening cytoplasm. Within this framework, we report spatial distributions of key proteins in wild-type (WT) mice and the effects on them of genetic deficiencies in 3 models of Bardet-Biedl syndrome.
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33
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34
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Templier T. MagC, magnetic collection of ultrathin sections for volumetric correlative light and electron microscopy. eLife 2019; 8:e45696. [PMID: 31294691 PMCID: PMC6697447 DOI: 10.7554/elife.45696] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/02/2019] [Indexed: 01/03/2023] Open
Abstract
The non-destructive collection of ultrathin sections on silicon wafers for post-embedding staining and volumetric correlative light and electron microscopy traditionally requires exquisite manual skills and is tedious and unreliable. In MagC introduced here, sample blocks are augmented with a magnetic resin enabling the remote actuation and collection of hundreds of sections on wafer. MagC allowed the correlative visualization of neuroanatomical tracers within their ultrastructural volumetric electron microscopy context.
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Affiliation(s)
- Thomas Templier
- Institute of NeuroinformaticsUniversity of Zurich and ETH ZurichZurichSwitzerland
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35
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Luo H, Wang G, Yuan L. A special three-layer step-index fiber for building compact STED systems. Sci Rep 2019; 9:8455. [PMID: 31186490 PMCID: PMC6560122 DOI: 10.1038/s41598-019-44905-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/23/2019] [Indexed: 11/09/2022] Open
Abstract
Up to now, most of stimulated-emission-depletion (STED) systems were lens-based bulky systems. Exchanging some spatial light paths with optical fiber components will make the systems more flexible and will benefit various fields. A big problem to achieve this goal is that the STED beam generated by the traditional method of bulky systems cannot be maintained in an optical fiber due to its birefringence. In this article, we will introduce a type of special optical fiber. With the special fiber, a dark hollow beam with doughnut-shaped focal spot and a concentric beam with Gaussian-shaped focal spot can be generated at the same time. Parameters of a sample and a compact STED system based on it are demonstrated.
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Affiliation(s)
- Hao Luo
- Key Laboratory of In-Fiber Integrated Optics, Ministry of Education, College of Science, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - Guiren Wang
- Department of Mechanical Engineering and Biomedical Engineering Program, University of South Carolina, Columbia, SC, 29208, USA
| | - Libo Yuan
- Photonics Research Center, Guilin University of Electronics Technology, Guilin, 541004, People's Republic of China.
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36
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Booth DG, Beckett AJ, Prior IA, Meijer D. SuperCLEM: an accessible correlative light and electron microscopy approach for investigation of neurons and glia in vitro. Biol Open 2019; 8:bio.042085. [PMID: 31110056 PMCID: PMC6550067 DOI: 10.1242/bio.042085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The rapid evolution of super-resolution light microscopy has narrowed the gap between light and electron microscopy, allowing the imaging of molecules and cellular structures at high resolution within their normal cellular and tissue context. Multimodal imaging approaches such as correlative light electron microscopy (CLEM) combine these techniques to create a tool with unique imaging capacity. However, these approaches are typically reserved for specialists, and their application to the analysis of neural tissue is challenging. Here we present SuperCLEM, a relatively simple approach that combines super-resolution fluorescence light microscopy (FLM), 3D electron microscopy (3D-EM) and rendering into 3D models. We demonstrate our workflow using neuron-glia cultures from which we first acquire high-resolution fluorescent light images of myelinated axons. After resin embedding and re-identification of the region of interest, serially aligned EM sections are acquired and imaged using a serial block face scanning electron microscope (SBF-SEM). The FLM and 3D-EM datasets are then combined to render 3D models of the myelinated axons. Thus, the SuperCLEM imaging pipeline is a useful new tool for researchers pursuing similar questions in neuronal and other complex tissue culture systems. Summary: We developed an advanced, accessible and adaptable correlative light and electron microscopy pipeline for study of neuron-glia cultures and demonstrate its power by deriving accurate 3D models of myelinated axons.
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Affiliation(s)
- Daniel G Booth
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Alison J Beckett
- Biomedical Electron Microscopy Unit, Department of Molecular and Cellular Biology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Ian A Prior
- Biomedical Electron Microscopy Unit, Department of Molecular and Cellular Biology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Dies Meijer
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
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Jimenez A, Friedl K, Leterrier C. About samples, giving examples: Optimized Single Molecule Localization Microscopy. Methods 2019; 174:100-114. [PMID: 31078795 DOI: 10.1016/j.ymeth.2019.05.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/28/2022] Open
Abstract
Super-resolution microscopy has profoundly transformed how we study the architecture of cells, revealing unknown structures and refining our view of cellular assemblies. Among the various techniques, the resolution of Single Molecule Localization Microscopy (SMLM) can reach the size of macromolecular complexes and offer key insights on their nanoscale arrangement in situ. SMLM is thus a demanding technique and taking advantage of its full potential requires specifically optimized procedures. Here we describe how we perform the successive steps of an SMLM workflow, focusing on single-color Stochastic Optical Reconstruction Microscopy (STORM) as well as multicolor DNA Points Accumulation for imaging in Nanoscale Topography (DNA-PAINT) of fixed samples. We provide detailed procedures for careful sample fixation and immunostaining of typical cellular structures: cytoskeleton, clathrin-coated pits, and organelles. We then offer guidelines for optimal imaging and processing of SMLM data in order to optimize reconstruction quality and avoid the generation of artifacts. We hope that the tips and tricks we discovered over the years and detail here will be useful for researchers looking to make the best possible SMLM images, a pre-requisite for meaningful biological discovery.
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Affiliation(s)
- Angélique Jimenez
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Karoline Friedl
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France; Abbelight, Paris, France
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Wang P, Chen S, Guo M, Peng S, Wang M, Chen M, Ma W, Zhang R, Su J, Rong X, Shi F, Xu T, Du J. Nanoscale magnetic imaging of ferritins in a single cell. SCIENCE ADVANCES 2019; 5:eaau8038. [PMID: 30989109 PMCID: PMC6457937 DOI: 10.1126/sciadv.aau8038] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 02/20/2019] [Indexed: 05/24/2023]
Abstract
The in situ measurement of the distribution of biomolecules inside a cell is one of the important goals in life science. Among various imaging techniques, magnetic imaging (MI) based on the nitrogen-vacancy (NV) center in diamond provides a powerful tool for the biomolecular research, while the nanometer-scale MI of intracellular proteins remains a challenge. Here, we use ferritin as a demonstration to realize the MI of endogenous proteins in a single cell using the NV center as the sensor. With the scanning, intracellular ferritins are imaged with a spatial resolution of ca. 10 nm, and ferritin-containing organelles are colocalized by correlative MI and electron microscopy. The approach paves the way for nanoscale MI of intracellular proteins.
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Affiliation(s)
- Pengfei Wang
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Sanyou Chen
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Maosen Guo
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Shijie Peng
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Mengqi Wang
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Ming Chen
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Wenchao Ma
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Rui Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jihu Su
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xing Rong
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Fazhan Shi
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Tao Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Jiangfeng Du
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
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Structural maturation of cortical perineuronal nets and their perforating synapses revealed by superresolution imaging. Proc Natl Acad Sci U S A 2019; 116:7071-7076. [PMID: 30890637 DOI: 10.1073/pnas.1817222116] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Parvalbumin-positive (PV+) interneurons play a pivotal role in orchestrating windows of experience-dependent brain plasticity during development. Critical period closure is marked by the condensation of a perineuronal net (PNN) tightly enwrapping subsets of PV+ neurons, both acting as a molecular brake on plasticity and maintaining mature PV+ cell signaling. As much of the molecular organization of PNNs exists at length scales near or below the diffraction limit of light microscopy, we developed a superresolution imaging and analysis platform to visualize the structural organization of PNNs and the synaptic inputs perforating them in primary visual cortex. We identified a structural trajectory of PNN maturation featuring a range of net structures, which was accompanied by an increase in Synaptotagmin-2 (Syt2) signals on PV+ cells suggestive of increased inhibitory input between PV+ neurons. The same structural trajectory was followed by PNNs both during normal development and under conditions of critical period delay by total sensory deprivation or critical period acceleration by deletion of MeCP2, the causative gene for Rett syndrome, despite shifted maturation levels under these perturbations. Notably, superresolution imaging further revealed a decrease in Syt2 signals alongside an increase in vesicular glutamate transporter-2 signals on PV+ cells in MeCP2-deficient animals, suggesting weaker recurrent inhibitory input between PV+ neurons and stronger thalamocortical excitatory inputs onto PV+ cells. These results imply a latent imbalanced circuit signature that might promote cortical silencing in Rett syndrome before the functional regression of vision.
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Xu J, Liu Y. Imaging Higher-order Chromatin Structures in Single Cells Using Stochastic Optical Reconstruction Microscopy. Bio Protoc 2019; 9:e3160. [PMID: 30873426 PMCID: PMC6414075 DOI: 10.21769/bioprotoc.3160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 11/02/2022] Open
Abstract
Higher-order chromatin organization shaped by epigenetic modifications influence the chromatin environment and subsequently regulate gene expression. Direct visualization of the higher-order chromatin structure at their epigenomic states is of great importance for understanding chromatin compaction and its subsequent effect on gene expression and various cellular processes. With the recent advances in super-resolution microscopy, the higher-order chromatin structure can now be directly visualized in situ down to the scale of ~30 nm. This protocol provides detailed description of super-resolution imaging of higher-order chromatin structure using stochastic optical reconstruction microscopy (STORM). We discussed fluorescence staining methods of DNA and histone proteins and crucial technical factors to obtain high-quality super-resolution images.
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Affiliation(s)
- Jianquan Xu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
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41
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Gruβmayer KS, Yserentant K, Herten DP. Photons in - numbers out: perspectives in quantitative fluorescence microscopy for in situ protein counting. Methods Appl Fluoresc 2019; 7:012003. [DOI: 10.1088/2050-6120/aaf2eb] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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42
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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43
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Abstract
Array tomography encompasses light and electron microscopy modalities that offer unparalleled opportunities to explore three-dimensional cellular architectures in extremely fine structural and molecular detail. Fluorescence array tomography achieves much higher resolution and molecular multiplexing than most other fluorescence microscopy methods, while electron array tomography can capture three-dimensional ultrastructure much more easily and rapidly than traditional serial-section electron microscopy methods. A correlative fluorescence/electron microscopy mode of array tomography furthermore offers a unique capacity to merge the molecular discrimination strengths of multichannel fluorescence microscopy with the ultrastructural imaging strengths of electron microscopy. This essay samples the first decade of array tomography, highlighting applications in neuroscience.
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44
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Sigal YM, Zhou R, Zhuang X. Visualizing and discovering cellular structures with super-resolution microscopy. Science 2018; 361:880-887. [PMID: 30166485 DOI: 10.1126/science.aau1044] [Citation(s) in RCA: 340] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Super-resolution microscopy has overcome a long-held resolution barrier-the diffraction limit-in light microscopy and enabled visualization of previously invisible molecular details in biological systems. Since their conception, super-resolution imaging methods have continually evolved and can now be used to image cellular structures in three dimensions, multiple colors, and living systems with nanometer-scale resolution. These methods have been applied to answer questions involving the organization, interaction, stoichiometry, and dynamics of individual molecular building blocks and their integration into functional machineries in cells and tissues. In this Review, we provide an overview of super-resolution methods, their state-of-the-art capabilities, and their constantly expanding applications to biology, with a focus on the latter. We will also describe the current technical challenges and future advances anticipated in super-resolution imaging.
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Affiliation(s)
- Yaron M Sigal
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Ruobo Zhou
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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45
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Lorenz-Guertin JM, Bambino MJ, Jacob TC. γ2 GABA AR Trafficking and the Consequences of Human Genetic Variation. Front Cell Neurosci 2018; 12:265. [PMID: 30190672 PMCID: PMC6116786 DOI: 10.3389/fncel.2018.00265] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/02/2018] [Indexed: 11/13/2022] Open
Abstract
GABA type A receptors (GABAARs) mediate the majority of fast inhibitory neurotransmission in the central nervous system (CNS). Most prevalent as heteropentamers composed of two α, two β, and a γ2 subunit, these ligand-gated ionotropic chloride channels are capable of extensive genetic diversity (α1-6, β1-3, γ1-3, δ, 𝜀, 𝜃, π, ρ1-3). Part of this selective GABAAR assembly arises from the critical role for γ2 in maintaining synaptic receptor localization and function. Accordingly, mutations in this subunit account for over half of the known epilepsy-associated genetic anomalies identified in GABAARs. Fundamental structure-function studies and cellular pathology investigations have revealed dynamic GABAAR trafficking and synaptic scaffolding as critical regulators of GABAergic inhibition. Here, we introduce in vitro and in vivo findings regarding the specific role of the γ2 subunit in receptor trafficking. We then examine γ2 subunit human genetic variation and assess disease related phenotypes and the potential role of altered GABAAR trafficking. Finally, we discuss new-age imaging techniques and their potential to provide novel insight into critical regulatory mechanisms of GABAAR function.
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Affiliation(s)
- Joshua M Lorenz-Guertin
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Matthew J Bambino
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Tija C Jacob
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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46
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Dharmat R, Eblimit A, Robichaux MA, Zhang Z, Nguyen TMT, Jung SY, He F, Jain A, Li Y, Qin J, Overbeek P, Roepman R, Mardon G, Wensel TG, Chen R. SPATA7 maintains a novel photoreceptor-specific zone in the distal connecting cilium. J Cell Biol 2018; 217:2851-2865. [PMID: 29899041 PMCID: PMC6080925 DOI: 10.1083/jcb.201712117] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/09/2018] [Accepted: 05/23/2018] [Indexed: 12/25/2022] Open
Abstract
Photoreceptor-specific ciliopathies often affect a structure that is considered functionally homologous to the ciliary transition zone (TZ) called the connecting cilium (CC). However, it is unclear how mutations in certain ciliary genes disrupt the photoreceptor CC without impacting the primary cilia systemically. By applying stochastic optical reconstruction microscopy technology in different genetic models, we show that the CC can be partitioned into two regions: the proximal CC (PCC), which is homologous to the TZ of primary cilia, and the distal CC (DCC), a photoreceptor-specific extension of the ciliary TZ. This specialized distal zone of the CC in photoreceptors is maintained by SPATA7, which interacts with other photoreceptor-specific ciliary proteins such as RPGR and RPGRIP1. The absence of Spata7 results in the mislocalization of DCC proteins without affecting the PCC protein complexes. This collapse results in destabilization of the axonemal microtubules, which consequently results in photoreceptor degeneration. These data provide a novel mechanism to explain how genetic disruption of ubiquitously present ciliary proteins exerts tissue-specific ciliopathy phenotypes.
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Affiliation(s)
- Rachayata Dharmat
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Aiden Eblimit
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Michael A Robichaux
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Zhixian Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Thanh-Minh T Nguyen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Feng He
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Antrix Jain
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Jun Qin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Paul Overbeek
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Graeme Mardon
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Theodore G Wensel
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Rui Chen
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
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47
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Combined expansion microscopy with structured illumination microscopy for analyzing protein complexes. Nat Protoc 2018; 13:1869-1895. [PMID: 30072723 DOI: 10.1038/s41596-018-0023-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 05/09/2018] [Indexed: 12/19/2022]
Abstract
Biologists have long been fascinated with the organization and function of intricate protein complexes. Therefore, techniques for precisely imaging protein complexes and the location of proteins within these complexes are critically important and often require multidisciplinary collaboration. A challenge in these explorations is the limited resolution of conventional light microscopy. However, a new microscopic technique has circumvented this resolution limit by making the biological sample larger, thus allowing for super-resolution of the enlarged structure. This 'expansion' is accomplished by embedding the sample in a hydrogel that, when exposed to water, uniformly expands. Here, we present a protocol that transforms thick expansion microscopy (ExM) hydrogels into sections that are physically expanded four times, creating samples that are compatible with the super-resolution technique structured illumination microscopy (SIM). This super-resolution ExM method (ExM-SIM) allows the analysis of the three-dimensional (3D) organization of multiprotein complexes at ~30-nm lateral (xy) resolution. This protocol details the steps necessary for analysis of protein localization using ExM-SIM, including antibody labeling, hydrogel preparation, protease digestion, post-digestion antibody labeling, hydrogel embedding with tissue-freezing medium (TFM), cryosectioning, expansion, image alignment, and particle averaging. We have used this approach for 3D mapping of in situ protein localization in the Drosophila synaptonemal complex (SC), but it can be readily adapted to study thick tissues such as brain and organs in various model systems. This procedure can be completed in 5 d.
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48
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Xu J, Ma H, Jin J, Uttam S, Fu R, Huang Y, Liu Y. Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells. Cell Rep 2018; 24:873-882. [PMID: 30044984 PMCID: PMC6154382 DOI: 10.1016/j.celrep.2018.06.085] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/18/2018] [Accepted: 06/20/2018] [Indexed: 01/10/2023] Open
Abstract
Histone modifications influence higher-order chromatin structures at individual epigenomic states and chromatin environments to regulate gene expression. However, genome-wide higher-order chromatin structures shaped by different histone modifications remain poorly characterized. With stochastic optical reconstruction microscopy (STORM), we characterized the higher-order chromatin structures at their epigenomic states, categorized into three major types in interphase: histone acetylation marks form spatially segregated nanoclusters, active histone methylation marks form spatially dispersed larger nanodomains, and repressive histone methylation marks form condensed large aggregates. These distinct structural characteristics are also observed in mitotic chromosomes. Furthermore, active histone marks coincide with less compact chromatin and exhibit a higher degree of co-localization with other active marks and RNA polymerase II (RNAP II), while repressive marks coincide with densely packed chromatin and spatially distant from repressive marks and active RNAP II. Taken together, super-resolution imaging reveals three distinct chromatin structures at various epigenomic states, which may be spatially coordinated to impact transcription.
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Affiliation(s)
- Jianquan Xu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Hongqiang Ma
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jingyi Jin
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA; School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China
| | - Shikhar Uttam
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Rao Fu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA; College of Chemical Engineering, Northeast Electric Power University, Jilin City, Jilin Province 132012, China
| | - Yi Huang
- Magee-Women's Research Institute, University of Pittsburgh Cancer Institute, 204 Craft Avenue, Pittsburgh, PA 15213, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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49
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Mlodzianoski MJ, Cheng-Hathaway PJ, Bemiller SM, McCray TJ, Liu S, Miller DA, Lamb BT, Landreth GE, Huang F. Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections. Nat Methods 2018; 15:583-586. [PMID: 30013047 PMCID: PMC6071422 DOI: 10.1038/s41592-018-0053-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/17/2018] [Indexed: 12/21/2022]
Abstract
Single Molecule Switching Nanoscopy (SMSN) beyond the coverslip surface poses significant challenges. The sample-induced aberrations distort and blur single-molecule emission patterns. Combining active point-spread function shaping and efficient adaptive optics enables robust 3D-SMSN imaging at large depths. This development allowed us to image through 30-μm thick brain sections, visualize the morphology and the nanoscale details of amyloid-β filaments in a mouse model of Alzheimer’s disease and reconstruct their volumetric arrangements.
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Affiliation(s)
- Michael J Mlodzianoski
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.,Centre for Dynamic Imaging, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Paul J Cheng-Hathaway
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Shane M Bemiller
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tyler J McCray
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sheng Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - David A Miller
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Bruce T Lamb
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Neurosciences, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Gary E Landreth
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA. .,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA. .,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA.
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50
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Hainsworth AH, Lee S, Foot P, Patel A, Poon WW, Knight AE. Super-resolution imaging of subcortical white matter using stochastic optical reconstruction microscopy (STORM) and super-resolution optical fluctuation imaging (SOFI). Neuropathol Appl Neurobiol 2018; 44:417-426. [PMID: 28696566 PMCID: PMC5835206 DOI: 10.1111/nan.12426] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 01/25/2023]
Abstract
AIMS The spatial resolution of light microscopy is limited by the wavelength of visible light (the 'diffraction limit', approximately 250 nm). Resolution of sub-cellular structures, smaller than this limit, is possible with super resolution methods such as stochastic optical reconstruction microscopy (STORM) and super-resolution optical fluctuation imaging (SOFI). We aimed to resolve subcellular structures (axons, myelin sheaths and astrocytic processes) within intact white matter, using STORM and SOFI. METHODS Standard cryostat-cut sections of subcortical white matter from donated human brain tissue and from adult rat and mouse brain were labelled, using standard immunohistochemical markers (neurofilament-H, myelin-associated glycoprotein, glial fibrillary acidic protein, GFAP). Image sequences were processed for STORM (effective pixel size 8-32 nm) and for SOFI (effective pixel size 80 nm). RESULTS In human, rat and mouse, subcortical white matter high-quality images for axonal neurofilaments, myelin sheaths and filamentous astrocytic processes were obtained. In quantitative measurements, STORM consistently underestimated width of axons and astrocyte processes (compared with electron microscopy measurements). SOFI provided more accurate width measurements, though with somewhat lower spatial resolution than STORM. CONCLUSIONS Super resolution imaging of intact cryo-cut human brain tissue is feasible. For quantitation, STORM can under-estimate diameters of thin fluorescent objects. SOFI is more robust. The greatest limitation for super-resolution imaging in brain sections is imposed by sample preparation. We anticipate that improved strategies to reduce autofluorescence and to enhance fluorophore performance will enable rapid expansion of this approach.
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Affiliation(s)
- A H Hainsworth
- Molecular and Clinical Sciences Research Institute, St Georges University of London, London, UK
- Neurology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - S Lee
- Cellular Pathology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - P Foot
- Cellular Pathology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - A Patel
- Cellular Pathology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - W W Poon
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - A E Knight
- National Physical Laboratory, Teddington, UK
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