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Samavat M, Bartol TM, Bromer C, Hubbard DD, Hanka DC, Kuwajima M, Mendenhall JM, Parker PH, Bowden JB, Abraham WC, Sejnowski TJ, Harris KM. Long-Term Potentiation Produces a Sustained Expansion of Synaptic Information Storage Capacity in Adult Rat Hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.574766. [PMID: 38260636 PMCID: PMC10802612 DOI: 10.1101/2024.01.12.574766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Long-term potentiation (LTP) has become a standard model for investigating synaptic mechanisms of learning and memory. Increasingly, it is of interest to understand how LTP affects the synaptic information storage capacity of the targeted population of synapses. Here, structural synaptic plasticity during LTP was explored using three-dimensional reconstruction from serial section electron microscopy. Storage capacity was assessed by applying a new analytical approach, Shannon information theory, to delineate the number of functionally distinguishable synaptic strengths. LTP was induced by delta-burst stimulation of perforant pathway inputs to the middle molecular layer of hippocampal dentate granule cells in adult rats. Spine head volumes were measured as predictors of synaptic strength and compared between LTP and control hemispheres at 30 min and 2 hr after the induction of LTP. Synapses from the same axon onto the same dendrite were used to determine the precision of synaptic plasticity based on the similarity of their physical dimensions. Shannon entropy was measured by exploiting the frequency of spine heads in functionally distinguishable sizes to assess the degree to which LTP altered the number of bits of information storage. Outcomes from these analyses reveal that LTP expanded storage capacity; the distribution of spine head volumes was increased from 2 bits in controls to 3 bits at 30 min and 2.7 bits at 2 hr after the induction of LTP. Furthermore, the distribution of spine head volumes was more uniform across the increased number of functionally distinguishable sizes following LTP, thus achieving more efficient use of coding space across the population of synapses.
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Affiliation(s)
- Mohammad Samavat
- Department of Electrical and Computer Engineering, Jacobs School of Engineering, UC San Diego
- Computational Neurobiology Laboratory, The Salk Institute for Biological Sciences, La Jolla, CA 92037
| | - Thomas M Bartol
- Computational Neurobiology Laboratory, The Salk Institute for Biological Sciences, La Jolla, CA 92037
| | - Cailey Bromer
- Computational Neurobiology Laboratory, The Salk Institute for Biological Sciences, La Jolla, CA 92037
| | - Dusten D Hubbard
- Center for Learning and Memory, The University of Texas at Austin, Austin, TX 78712
| | - Dakota C Hanka
- Center for Learning and Memory, The University of Texas at Austin, Austin, TX 78712
| | - Masaaki Kuwajima
- Center for Learning and Memory, The University of Texas at Austin, Austin, TX 78712
| | - John M Mendenhall
- Center for Learning and Memory, The University of Texas at Austin, Austin, TX 78712
| | - Patrick H Parker
- Center for Learning and Memory, The University of Texas at Austin, Austin, TX 78712
| | - Jared B Bowden
- Center for Learning and Memory, The University of Texas at Austin, Austin, TX 78712
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712
| | - Wickliffe C Abraham
- Department of Psychology and Brain Health Research Centre, University of Otago, Dunedin, 9016, New Zealand
| | - Terrence J Sejnowski
- Computational Neurobiology Laboratory, The Salk Institute for Biological Sciences, La Jolla, CA 92037
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Kristen M Harris
- Center for Learning and Memory, The University of Texas at Austin, Austin, TX 78712
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712
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2
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Fiedler KR, Olszta MJ, Yano KH, Doty C, Hopkins D, Akers S, Spurgeon SR. Evaluating Stage Motion for Automated Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1931-1939. [PMID: 37832144 DOI: 10.1093/micmic/ozad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 08/15/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
Precise control is an essential and elusive quality of emerging self-driving transmission electron microscopes (TEMs). It is widely understood these instruments must be capable of performing rapid, high-volume, and arbitrary movements for practical self-driving operation. However, stage movements are difficult to automate at scale, owing to mechanical instability, hysteresis, and thermal drift. Such difficulties pose major barriers to artificial intelligence-directed microscope designs that require repeatable, precise movements. To guide design of emerging instruments, it is necessary to understand the behavior of existing mechanisms to identify rate limiting steps for full autonomy. Here, we describe a general framework to evaluate stage motion in any TEM. We define metrics to evaluate stage degrees of freedom, propose solutions to improve performance, and comment on fundamental limits to automated experimentation using present hardware.
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Affiliation(s)
- Kevin R Fiedler
- College of Arts and Sciences, Washington State University-Tri-Cities, Richland, WA 99354, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Matthew J Olszta
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Kayla H Yano
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Christina Doty
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Derek Hopkins
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sarah Akers
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Steven R Spurgeon
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Department of Physics, University of Washington, Seattle, WA 98195, USA
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3
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Pérez-Garza J, Parrish-Mulliken E, Deane Z, Ostroff LE. Rehydration of Freeze Substituted Brain Tissue for Pre-embedding Immunoelectron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1694-1704. [PMID: 37584524 PMCID: PMC10541149 DOI: 10.1093/micmic/ozad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/27/2023] [Accepted: 07/16/2023] [Indexed: 08/17/2023]
Abstract
Electron microscopy (EM) volume reconstruction is a powerful tool for investigating the fundamental structure of brain circuits, but the full potential of this technique is limited by the difficulty of integrating molecular information. High quality ultrastructural preservation is necessary for EM reconstruction, and intact, highly contrasted cell membranes are essential for following small neuronal processes through serial sections. Unfortunately, the antibody labeling methods used to identify most endogenous molecules result in compromised morphology, especially of membranes. Cryofixation can produce superior morphological preservation and has the additional advantage of allowing indefinite storage of valuable samples. We have developed a method based on cryofixation that allows sensitive immunolabeling of endogenous molecules, preserves excellent ultrastructure, and is compatible with high-contrast staining for serial EM reconstruction.
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Affiliation(s)
- Janeth Pérez-Garza
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Rd. Unit 3156, Storrs, CT 06269-3156, USA
| | - Emily Parrish-Mulliken
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Rd. Unit 3156, Storrs, CT 06269-3156, USA
| | - Zachary Deane
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Rd. Unit 3156, Storrs, CT 06269-3156, USA
| | - Linnaea E Ostroff
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Rd. Unit 3156, Storrs, CT 06269-3156, USA
- Connecticut Institute for the Brain and Cognitive Sciences, University of Connecticut, 337 Mansfield Rd. Unit 1272, Storrs, CT 06269-1272, USA
- Institute of Materials Science, University of Connecticut, 25 King Hill Rd. Unit 3136, Storrs, CT 06269-3136, USA
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Kleinjan MS, Buchta WC, Ogelman R, Hwang IW, Kuwajima M, Hubbard DD, Kareemo DJ, Prikhodko O, Olah SL, Gomez Wulschner LE, Abraham WC, Franco SJ, Harris KM, Oh WC, Kennedy MJ. Dually innervated dendritic spines develop in the absence of excitatory activity and resist plasticity through tonic inhibitory crosstalk. Neuron 2023; 111:362-371.e6. [PMID: 36395772 PMCID: PMC9899020 DOI: 10.1016/j.neuron.2022.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 07/13/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022]
Abstract
Dendritic spines can be directly connected to both inhibitory and excitatory presynaptic terminals, resulting in nanometer-scale proximity of opposing synaptic functions. While dually innervated spines (DiSs) are observed throughout the central nervous system, their developmental timeline and functional properties remain uncharacterized. Here we used a combination of serial section electron microscopy, live imaging, and local synapse activity manipulations to investigate DiS development and function in rodent hippocampus. Dual innervation occurred early in development, even on spines where the excitatory input was locally silenced. Synaptic NMDA receptor currents were selectively reduced at DiSs through tonic GABAB receptor signaling. Accordingly, spine enlargement normally associated with long-term potentiation on singly innervated spines (SiSs) was blocked at DiSs. Silencing somatostatin interneurons or pharmacologically blocking GABABRs restored NMDA receptor function and structural plasticity to levels comparable to neighboring SiSs. Thus, hippocampal DiSs are stable structures where function and plasticity are potently regulated by nanometer-scale GABAergic signaling.
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Affiliation(s)
- Mason S Kleinjan
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - William C Buchta
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Roberto Ogelman
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - In-Wook Hwang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Masaaki Kuwajima
- Department of Neuroscience, University of Texas at Austin, Austin, TX 78712, USA
| | - Dusten D Hubbard
- Department of Neuroscience, University of Texas at Austin, Austin, TX 78712, USA
| | - Dean J Kareemo
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Olga Prikhodko
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Samantha L Olah
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Luis E Gomez Wulschner
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Wickliffe C Abraham
- Department of Psychology, Brain Health Research Centre, University of Otago, Dunedin, New Zealand
| | - Santos J Franco
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kristen M Harris
- Department of Neuroscience, University of Texas at Austin, Austin, TX 78712, USA
| | - Won Chan Oh
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Matthew J Kennedy
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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Harris KM, Hubbard DD, Kuwajima M, Abraham WC, Bourne JN, Bowden JB, Haessly A, Mendenhall JM, Parker PH, Shi B, Spacek J. Dendritic Spine Density Scales with Microtubule Number in Rat Hippocampal Dendrites. Neuroscience 2022; 489:84-97. [PMID: 35218884 PMCID: PMC9038701 DOI: 10.1016/j.neuroscience.2022.02.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 12/14/2022]
Abstract
Microtubules deliver essential resources to and from synapses. Three-dimensional reconstructions in rat hippocampus reveal a sampling bias regarding spine density that needs to be controlled for dendrite caliber and resource delivery based on microtubule number. The strength of this relationship varies across dendritic arbors, as illustrated for area CA1 and dentate gyrus. In both regions, proximal dendrites had more microtubules than distal dendrites. For CA1 pyramidal cells, spine density was greater on thicker than thinner dendrites in stratum radiatum, or on the more uniformly thin terminal dendrites in stratum lacunosum moleculare. In contrast, spine density was constant across the cone shaped arbor of tapering dendrites from dentate granule cells. These differences suggest that thicker dendrites supply microtubules to subsequent dendritic branches and local dendritic spines, whereas microtubules in thinner dendrites need only provide resources to local spines. Most microtubules ran parallel to dendrite length and associated with long, presumably stable mitochondria, which occasionally branched into lateral dendritic branches. Short, presumably mobile, mitochondria were tethered to microtubules that bent and appeared to direct them into a thin lateral branch. Prior work showed that dendritic segments with the same number of microtubules had elevated resources in subregions of their dendritic shafts where spine synapses had enlarged, and spine clusters had formed. Thus, additional microtubules were not required for redistribution of resources locally to growing spines or synapses. These results provide new understanding about the potential for microtubules to regulate resource delivery to and from dendritic branches and locally among dendritic spines.
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Affiliation(s)
- Kristen M Harris
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, TX, United States.
| | - Dusten D Hubbard
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, TX, United States
| | - Masaaki Kuwajima
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, TX, United States
| | - Wickliffe C Abraham
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, TX, United States
| | - Jennifer N Bourne
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, TX, United States
| | - Jared B Bowden
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, TX, United States
| | - Andrea Haessly
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, TX, United States
| | - John M Mendenhall
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, TX, United States
| | - Patrick H Parker
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, TX, United States
| | - Bitao Shi
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, TX, United States
| | - Josef Spacek
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, TX, United States
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6
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Lewczuk B, Szyryńska N. Field-Emission Scanning Electron Microscope as a Tool for Large-Area and Large-Volume Ultrastructural Studies. Animals (Basel) 2021; 11:ani11123390. [PMID: 34944167 PMCID: PMC8698110 DOI: 10.3390/ani11123390] [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: 10/31/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Ultrastructural studies of cells and tissues are usually performed using transmission electron microscopy (TEM), which enables imaging at the highest possible resolution. The weak point of TEM is the limited ability to analyze the ultrastructure of large areas and volumes of biological samples. This limitation can be overcome by using modern field-emission scanning electron microscopy (FE-SEM) with high-sensitivity detection, which enables the creation of TEM-like images from the flat surfaces of resin-embedded biological specimens. Several FE-SEM-based techniques for two- and three-dimensional ultrastructural studies of cells, tissues, organs, and organisms have been developed in the 21st century. These techniques have created a new era in structural biology and have changed the role of the scanning electron microscope (SEM) in biological and medical laboratories. Since the premiere of the first commercially available SEM in 1965, these instruments were used almost exclusively to obtain topographical information over a large range of magnifications. Currently, FE-SEM offers many attractive possibilities in the studies of cell and tissue ultrastructure, and they are presented in this review. Abstract The development of field-emission scanning electron microscopes for high-resolution imaging at very low acceleration voltages and equipped with highly sensitive detectors of backscattered electrons (BSE) has enabled transmission electron microscopy (TEM)-like imaging of the cut surfaces of tissue blocks, which are impermeable to the electron beam, or tissue sections mounted on the solid substrates. This has resulted in the development of methods that simplify and accelerate ultrastructural studies of large areas and volumes of biological samples. This article provides an overview of these methods, including their advantages and disadvantages. The imaging of large sample areas can be performed using two methods based on the detection of transmitted electrons or BSE. Effective imaging using BSE requires special fixation and en bloc contrasting of samples. BSE imaging has resulted in the development of volume imaging techniques, including array tomography (AT) and serial block-face imaging (SBF-SEM). In AT, serial ultrathin sections are collected manually on a solid substrate such as a glass and silicon wafer or automatically on a tape using a special ultramicrotome. The imaging of serial sections is used to obtain three-dimensional (3D) information. SBF-SEM is based on removing the top layer of a resin-embedded sample using an ultramicrotome inside the SEM specimen chamber and then imaging the exposed surface with a BSE detector. The steps of cutting and imaging the resin block are repeated hundreds or thousands of times to obtain a z-stack for 3D analyses.
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7
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Shortened tethering filaments stabilize presynaptic vesicles in support of elevated release probability during LTP in rat hippocampus. Proc Natl Acad Sci U S A 2021; 118:2018653118. [PMID: 33875591 DOI: 10.1073/pnas.2018653118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Long-term potentiation (LTP) is a cellular mechanism of learning and memory that results in a sustained increase in the probability of vesicular release of neurotransmitter. However, previous work in hippocampal area CA1 of the adult rat revealed that the total number of vesicles per synapse decreases following LTP, seemingly inconsistent with the elevated release probability. Here, electron-microscopic tomography (EMT) was used to assess whether changes in vesicle density or structure of vesicle tethering filaments at the active zone might explain the enhanced release probability following LTP. The spatial relationship of vesicles to the active zone varies with functional status. Tightly docked vesicles contact the presynaptic membrane, have partially formed SNARE complexes, and are primed for release of neurotransmitter upon the next action potential. Loosely docked vesicles are located within 8 nm of the presynaptic membrane where SNARE complexes begin to form. Nondocked vesicles comprise recycling and reserve pools. Vesicles are tethered to the active zone via filaments composed of molecules engaged in docking and release processes. The density of tightly docked vesicles was increased 2 h following LTP compared to control stimulation, whereas the densities of loosely docked or nondocked vesicles congregating within 45 nm above the active zones were unchanged. The tethering filaments on all vesicles were shorter and their attachment sites shifted closer to the active zone. These findings suggest that tethering filaments stabilize more vesicles in the primed state. Such changes would facilitate the long-lasting increase in release probability following LTP.
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8
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Fang L, Monroe F, Novak SW, Kirk L, Schiavon CR, Yu SB, Zhang T, Wu M, Kastner K, Latif AA, Lin Z, Shaw A, Kubota Y, Mendenhall J, Zhang Z, Pekkurnaz G, Harris K, Howard J, Manor U. Deep learning-based point-scanning super-resolution imaging. Nat Methods 2021; 18:406-416. [PMID: 33686300 PMCID: PMC8035334 DOI: 10.1038/s41592-021-01080-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/28/2021] [Indexed: 01/28/2023]
Abstract
Point-scanning imaging systems are among the most widely used tools for high-resolution cellular and tissue imaging, benefiting from arbitrarily defined pixel sizes. The resolution, speed, sample preservation and signal-to-noise ratio (SNR) of point-scanning systems are difficult to optimize simultaneously. We show these limitations can be mitigated via the use of deep learning-based supersampling of undersampled images acquired on a point-scanning system, which we term point-scanning super-resolution (PSSR) imaging. We designed a 'crappifier' that computationally degrades high SNR, high-pixel resolution ground truth images to simulate low SNR, low-resolution counterparts for training PSSR models that can restore real-world undersampled images. For high spatiotemporal resolution fluorescence time-lapse data, we developed a 'multi-frame' PSSR approach that uses information in adjacent frames to improve model predictions. PSSR facilitates point-scanning image acquisition with otherwise unattainable resolution, speed and sensitivity. All the training data, models and code for PSSR are publicly available at 3DEM.org.
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Affiliation(s)
- Linjing Fang
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Fred Monroe
- Wicklow AI Medical Research Initiative, San Francisco, CA, USA
| | - Sammy Weiser Novak
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Lyndsey Kirk
- Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, Austin, TX, USA
| | - Cara R Schiavon
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Seungyoon B Yu
- Neurobiology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tong Zhang
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Melissa Wu
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Kyle Kastner
- Montreal Institute for Learning Algorithms, Université de Montréal, Montréal, Canada
| | - Alaa Abdel Latif
- Fast.AI, University of San Francisco Data Institute, San Francisco, CA, USA
| | - Zijun Lin
- Fast.AI, University of San Francisco Data Institute, San Francisco, CA, USA
| | - Andrew Shaw
- Fast.AI, University of San Francisco Data Institute, San Francisco, CA, USA
| | - Yoshiyuki Kubota
- Division of Cerebral Circuitry, National Institute for Physiological Sciences, Okazaki, Japan
| | - John Mendenhall
- Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, Austin, TX, USA
| | - Zhao Zhang
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | - Gulcin Pekkurnaz
- Neurobiology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kristen Harris
- Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, Austin, TX, USA
| | - Jeremy Howard
- Fast.AI, University of San Francisco Data Institute, San Francisco, CA, USA
| | - Uri Manor
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA.
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9
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Döring CC, Kumar S, Tumu SC, Kourtesis I, Hausen H. The visual pigment xenopsin is widespread in protostome eyes and impacts the view on eye evolution. eLife 2020; 9:55193. [PMID: 32880369 PMCID: PMC7529461 DOI: 10.7554/elife.55193] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 09/01/2020] [Indexed: 12/31/2022] Open
Abstract
Photoreceptor cells in the eyes of Bilateria are often classified into microvillar cells with rhabdomeric opsin and ciliary cells with ciliary opsin, each type having specialized molecular components and physiology. First data on the recently discovered xenopsin point towards a more complex situation in protostomes. In this study, we provide clear evidence that xenopsin enters cilia in the eye of the larval bryozoan Tricellaria inopinata and triggers phototaxis. As reported from a mollusc, we find xenopsin coexpressed with rhabdomeric-opsin in eye photoreceptor cells bearing both microvilli and cilia in larva of the annelid Malacoceros fuliginosus. This is the first organism known to have both xenopsin and ciliary opsin, showing that these opsins are not necessarily mutually exclusive. Compiling existing data, we propose that xenopsin may play an important role in many protostome eyes and provides new insights into the function, evolution, and possible plasticity of animal eye photoreceptor cells.
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Affiliation(s)
| | - Suman Kumar
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Sharat Chandra Tumu
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Ioannis Kourtesis
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Harald Hausen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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10
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Zuidema W, Kruit P. Transmission imaging on a scintillator in a scanning electron microscope. Ultramicroscopy 2020; 218:113055. [PMID: 32731131 DOI: 10.1016/j.ultramic.2020.113055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/15/2020] [Accepted: 06/21/2020] [Indexed: 11/26/2022]
Abstract
Large area electron microscopy (EM) imaging has long been difficult due to fundamental limits in throughput for conventional electron microscopes. New developments in transmission electron microscopy and multi-beam scanning electron microscopy (MBSEM) imaging have however made it possible to generate large EM datasets [1,2,3]. This article describes a transmission imaging technique that is suitable for a MBSEM as it allows for a relatively straightforward way of separating the signals generated by each beam. The technique places a thin (50nm-200nm) tissue section directly on top of a coated scintillator. The electrons that are transmitted through the section generate light in the scintillator which is collected by a high NA objective and imaged onto a photon detector. This article gives a model for the contrast-to-noise (CNR) and signal-to-noise (SNR) ratio that is to be expected for this imaging technique. These parameters were calculated using Monte-Carlo simulations. It was found that the CNR increases when decreasing landing energy and SNR increases with increasing landing energy. These two trends cause that there is an intermediate energy where imaging performance is best. The energy of this optimum was calculated for various levels of heavy metal staining, section thickness, coating material, coating thickness and light collection efficiency. The model was verified experimentally on a synthetic sample.
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Affiliation(s)
- Wilco Zuidema
- Delft University of Technology, Mekelweg 5, 2628CD, Delft, The Netherlands.
| | - Pieter Kruit
- Delft University of Technology, Mekelweg 5, 2628CD, Delft, The Netherlands
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11
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Capillary-Based and Stokes-Based Trapping of Serial Sections for Scalable 3D-EM Connectomics. eNeuro 2020; 7:ENEURO.0328-19.2019. [PMID: 32094293 PMCID: PMC7174874 DOI: 10.1523/eneuro.0328-19.2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 11/23/2022] Open
Abstract
Serial section electron microscopy (ssEM), a technique where volumes of tissue can be anatomically reconstructed by imaging consecutive tissue slices, has proven to be a powerful tool for the investigation of brain anatomy. Between the process of cutting the slices, or “sections,” and imaging them, however, handling 10°−106 delicate sections remains a bottleneck in ssEM, especially for batches in the “mesoscale” regime, i.e., 102–103 sections. We present a tissue section handling device that transports and positions sections, accurately and repeatability, for automated, robotic section pick-up and placement onto an imaging substrate. The device interfaces with a conventional ultramicrotomy diamond knife, accomplishing in-line, exact-constraint trapping of sections with 100-μm repeatability. An associated mathematical model includes capillary-based and Stokes-based forces, accurately describing observed behavior and fundamentally extends the modeling of water-air interface forces. Using the device, we demonstrate and describe the limits of reliable handling of hundreds of slices onto a variety of electron and light microscopy substrates without significant defects (n = 8 datasets composed of 126 serial sections in an automated fashion with an average loss rate and throughput of 0.50% and 63 s/section, respectively. In total, this work represents an automated mesoscale serial sectioning system for scalable 3D-EM connectomics.
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12
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Ultrastructure of light-activated axons following optogenetic stimulation to produce late-phase long-term potentiation. PLoS One 2020; 15:e0226797. [PMID: 31940316 PMCID: PMC6961864 DOI: 10.1371/journal.pone.0226797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/04/2019] [Indexed: 12/03/2022] Open
Abstract
Analysis of neuronal compartments has revealed many state-dependent changes in geometry but establishing synapse-specific mechanisms at the nanoscale has proven elusive. We co-expressed channelrhodopsin2-GFP and mAPEX2 in a subset of hippocampal CA3 neurons and used trains of light to induce late-phase long-term potentiation (L-LTP) in area CA1. L-LTP was shown to be specific to the labeled axons by severing CA3 inputs, which prevented back-propagating recruitment of unlabeled axons. Membrane-associated mAPEX2 tolerated microwave-enhanced chemical fixation and drove tyramide signal amplification to deposit Alexa Fluor dyes in the light-activated axons. Subsequent post-embedding immunogold labeling resulted in outstanding ultrastructure and clear distinctions between labeled (activated), and unlabeled axons without obscuring subcellular organelles. The gold-labeled axons in potentiated slices were reconstructed through serial section electron microscopy; presynaptic vesicles and other constituents could be quantified unambiguously. The genetic specification, reliable physiology, and compatibility with established methods for ultrastructural preservation make this an ideal approach to link synapse ultrastructure and function in intact circuits.
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13
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Affiliation(s)
- Kristen M Harris
- Department of Neuroscience, Center for Learning and Memory, University of Texas at Austin, Austin, Texas 78712
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14
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Ilett M, Wills J, Rees P, Sharma S, Micklethwaite S, Brown A, Brydson R, Hondow N. Application of automated electron microscopy imaging and machine learning to characterise and quantify nanoparticle dispersion in aqueous media. J Microsc 2019; 279:177-184. [PMID: 31823372 PMCID: PMC7496512 DOI: 10.1111/jmi.12853] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/06/2019] [Accepted: 12/07/2019] [Indexed: 12/11/2022]
Abstract
For many nanoparticle applications it is important to understand dispersion in liquids. For nanomedicinal and nanotoxicological research this is complicated by the often complex nature of the biological dispersant and ultimately this leads to severe limitations in the analysis of the nanoparticle dispersion by light scattering techniques. Here we present an alternative analysis and associated workflow which utilises electron microscopy. The need to collect large, statistically relevant datasets by imaging vacuum dried, plunge frozen aliquots of suspension was accomplished by developing an automated STEM imaging protocol implemented in an SEM fitted with a transmission detector. Automated analysis of images of agglomerates was achieved by machine learning using two free open‐source software tools: CellProfiler and ilastik. The specific results and overall workflow described enable accurate nanoparticle agglomerate analysis of particles suspended in aqueous media containing other potential confounding components such as salts, vitamins and proteins. Lay Description In order to further advance studies in both nanomedicine and nanotoxicology, we need to continue to understand the dispersion of nanoparticles in biological fluids. These biological environments often contain a number of components such as salts, vitamins and proteins which can lead to difficulties when using traditional techniques to monitor dispersion. Here we present an alternative analysis which utilises electron microscopy. In order to use this approach statistically relevant large image datasets were collected from appropriately prepared samples of nanoparticle suspensions by implementing an automated imaging protocol. Automated analysis of these images was achieved through machine learning using two readily accessible freeware; CellProfiler and ilastik. The workflow presented enables accurate nanoparticle dispersion analysis of particles suspended in more complex biological media.
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Affiliation(s)
- M Ilett
- School of Chemical and Process Engineering, University of Leeds, Leeds, U.K
| | - J Wills
- Department of Veterinary Medicine, University of Cambridge, Cambridge, U.K
| | - P Rees
- Centre for Nanohealth, Swansea University, College of Engineering, Swansea, U.K
| | - S Sharma
- School of Chemical and Process Engineering, University of Leeds, Leeds, U.K
| | - S Micklethwaite
- School of Chemical and Process Engineering, University of Leeds, Leeds, U.K
| | - A Brown
- School of Chemical and Process Engineering, University of Leeds, Leeds, U.K
| | - R Brydson
- School of Chemical and Process Engineering, University of Leeds, Leeds, U.K
| | - N Hondow
- School of Chemical and Process Engineering, University of Leeds, Leeds, U.K
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15
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Kubota Y. Editorial: Electron-Microscopy-Based Tools for Imaging Cellular Circuits and Organisms. Front Neural Circuits 2019; 13:64. [PMID: 31680878 PMCID: PMC6797905 DOI: 10.3389/fncir.2019.00064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 09/24/2019] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yoshiyuki Kubota
- Division of Cerebral Circuitry, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
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16
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Balancing Extrasynaptic Excitation and Synaptic Inhibition within Olfactory Bulb Glomeruli. eNeuro 2019; 6:ENEURO.0247-19.2019. [PMID: 31345999 PMCID: PMC6709216 DOI: 10.1523/eneuro.0247-19.2019] [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] [Received: 06/26/2019] [Revised: 07/15/2019] [Accepted: 07/22/2019] [Indexed: 12/31/2022] Open
Abstract
Glutamatergic transmission in the brain typically occurs at well-defined synaptic connections, but increasing evidence indicates that neural excitation can also occur through activation of “extrasynaptic” glutamate receptors. Here, we investigated the underlying mechanisms and functional properties of extrasynaptic signals that are part of a feedforward path of information flow in the olfactory bulb. This pathway involves glutamatergic interneurons, external tufted cells (eTCs), that are excited by olfactory sensory neurons (OSNs) and in turn excite output mitral cells (MCs) extrasynaptically. Using pair-cell and triple-cell recordings in rat bulb slices (of either sex), combined with ultrastructural approaches, we first present evidence that eTC-to-MC signaling results from “spillover” of glutamate released at eTC synapses onto GABAergic periglomerular (PG) cells in glomeruli. Thus, feedforward excitation is an indirect result of and must cooccur with activation of inhibitory circuitry. Next, to examine the dynamics of the competing signals, we assayed the relationship between the number of spikes in eTCs and excitation of MCs or PG cells in pair-cell recordings. This showed that extrasynaptic excitation in MCs is very weak due to single spikes but rises sharply and supralinearly with increasing spikes, differing from sublinear behavior for synaptic excitation of PG cells. Similar dynamics leading to a preference for extrasynaptic excitation were also observed during recordings of extrasynaptic and inhibitory currents in response to OSN input of increasing magnitude. The observed alterations in the balance between extrasynaptic excitation and inhibition in glomeruli with stimulus strength could underlie an intraglomerular mechanism for olfactory contrast enhancement.
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17
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Holm J. Scattering intensity distribution dependence on collection angles in annular dark-field STEM-in-SEM images. Ultramicroscopy 2018; 195:12-20. [DOI: 10.1016/j.ultramic.2018.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/04/2018] [Accepted: 06/10/2018] [Indexed: 10/14/2022]
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18
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Kubota Y, Sohn J, Kawaguchi Y. Large Volume Electron Microscopy and Neural Microcircuit Analysis. Front Neural Circuits 2018; 12:98. [PMID: 30483066 PMCID: PMC6240581 DOI: 10.3389/fncir.2018.00098] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/17/2018] [Indexed: 12/23/2022] Open
Abstract
One recent technical innovation in neuroscience is microcircuit analysis using three-dimensional reconstructions of neural elements with a large volume Electron microscopy (EM) data set. Large-scale data sets are acquired with newly-developed electron microscope systems such as automated tape-collecting ultramicrotomy (ATUM) with scanning EM (SEM), serial block-face EM (SBEM) and focused ion beam-SEM (FIB-SEM). Currently, projects are also underway to develop computer applications for the registration and segmentation of the serially-captured electron micrographs that are suitable for analyzing large volume EM data sets thoroughly and efficiently. The analysis of large volume data sets can bring innovative research results. These recently available techniques promote our understanding of the functional architecture of the brain.
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Affiliation(s)
- Yoshiyuki Kubota
- Division of Cerebral Circuitry, National Institute for Physiological Sciences (NIPS), Okazaki, Japan
- Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Jaerin Sohn
- Division of Cerebral Circuitry, National Institute for Physiological Sciences (NIPS), Okazaki, Japan
- Research Fellow of Japan Society for the Promotion of Science (JSPS), Tokyo, Japan
| | - Yasuo Kawaguchi
- Division of Cerebral Circuitry, National Institute for Physiological Sciences (NIPS), Okazaki, Japan
- Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
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19
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Lee TJ, Kumar A, Balwani AH, Brittain D, Kinn S, Tovey CA, Dyer EL, da Costa NM, Reid RC, Forest CR, Bumbarger DJ. Large-scale neuroanatomy using LASSO: Loop-based Automated Serial Sectioning Operation. PLoS One 2018; 13:e0206172. [PMID: 30352088 PMCID: PMC6198950 DOI: 10.1371/journal.pone.0206172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/08/2018] [Indexed: 12/01/2022] Open
Abstract
Serial section transmission electron microscopy (ssTEM) is the most promising tool for investigating the three-dimensional anatomy of the brain with nanometer resolution. Yet as the field progresses to larger volumes of brain tissue, new methods for high-yield, low-cost, and high-throughput serial sectioning are required. Here, we introduce LASSO (Loop-based Automated Serial Sectioning Operation), in which serial sections are processed in “batches.” Batches are quantized groups of individual sections that, in LASSO, are cut with a diamond knife, picked up from an attached waterboat, and placed onto microfabricated TEM substrates using rapid, accurate, and repeatable robotic tools. Additionally, we introduce mathematical models for ssTEM with respect to yield, throughput, and cost to access ssTEM scalability. To validate the method experimentally, we processed 729 serial sections of human brain tissue (~40 nm x 1 mm x 1 mm). Section yield was 727/729 (99.7%). Sections were placed accurately and repeatably (x-direction: -20 ± 110 μm (1 s.d.), y-direction: 60 ± 150 μm (1 s.d.)) with a mean cycle time of 43 s ± 12 s (1 s.d.). High-magnification (2.5 nm/px) TEM imaging was conducted to measure the image quality. We report no significant distortion, information loss, or substrate-derived artifacts in the TEM images. Quantitatively, the edge spread function across vesicle edges and image contrast were comparable, suggesting that LASSO does not negatively affect image quality. In total, LASSO compares favorably with traditional serial sectioning methods with respect to throughput, yield, and cost for large-scale experiments, and represents a flexible, scalable, and accessible technology platform to enable the next generation of neuroanatomical studies.
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Affiliation(s)
- Timothy J. Lee
- Georgia Institute of Technology, G. W. Woodruff School of Mechanical Engineering, Atlanta, GA, United States of America
- * E-mail:
| | - Aditi Kumar
- Georgia Institute of Technology, G. W. Woodruff School of Mechanical Engineering, Atlanta, GA, United States of America
| | - Aishwarya H. Balwani
- Georgia Institute of Technology, School of Electrical and Computer Engineering, Atlanta, GA, United States of America
| | - Derrick Brittain
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Sam Kinn
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Craig A. Tovey
- Georgia Institute of Technology, H. Milton Stewart School of Industrial & Systems Engineering, Atlanta, GA, United States of America
| | - Eva L. Dyer
- Georgia Institute of Technology, School of Electrical and Computer Engineering, Atlanta, GA, United States of America
- Georgia Institute of Technology, Coulter Department of Biomedical Engineering, Atlanta, GA, United States of America
| | - Nuno M. da Costa
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - R. Clay Reid
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Craig R. Forest
- Georgia Institute of Technology, G. W. Woodruff School of Mechanical Engineering, Atlanta, GA, United States of America
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20
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Lara HH, Guisbiers G, Mendoza J, Mimun LC, Vincent BA, Lopez-Ribot JL, Nash KL. Synergistic antifungal effect of chitosan-stabilized selenium nanoparticles synthesized by pulsed laser ablation in liquids against Candida albicans biofilms. Int J Nanomedicine 2018; 13:2697-2708. [PMID: 29760550 PMCID: PMC5937483 DOI: 10.2147/ijn.s151285] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Candida albicans is a major opportunistic fungal pathogen. One of the most important virulence factors that contribute to the pathogenesis of candidiasis is its ability to form biofilms. A key characteristic of Candida biofilms is their resistance to antifungal agents. Due to significant morbidity and mortality rates related to biofilm-associated drug resistance, there is an urgency to develop novel nanotechnology-based approaches preventing biofilm-related infections. METHODS In this study, we report, for the first time, the synthesis of selenium nanoparticles by irradiating selenium pellets by nanosecond pulsed laser ablation in liquid chitosan as a capping agent. Synergy of the fungicidal effect of selenium nanoparticles and chitosan was quantified by the combination index theorem of Chou-Talalay. RESULTS This drug combination resulted in a potent fungicidal effect against a preformed C. albicans biofilm in a dose-response manner. By advanced electron microscopy techniques, we documented the adhesive and permeabilizing properties of chitosan, therefore allowing selenium nanoparticles to enter as the cell wall of the yeast became disrupted and distorted. Most importantly, we demonstrated a potent quantitative synergistic effect when compounds such as selenium and chitosan are combined. CONCLUSION These chitosan-stabilized selenium nanoparticles could be used for ex vivo applications such as sterilizers for surfaces and biomedical devices.
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Affiliation(s)
- Humberto H Lara
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Gregory Guisbiers
- Department of Physics and Astronomy, University of Arkansas at Little Rock, Little Rock, AR, USA
| | - Jonathan Mendoza
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Lawrence C Mimun
- US Army Engineer Research & Development Center, Vicksburg, MS, USA
| | - Brandy A Vincent
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Jose L Lopez-Ribot
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Kelly L Nash
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
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21
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Kubota Y, Sohn J, Hatada S, Schurr M, Straehle J, Gour A, Neujahr R, Miki T, Mikula S, Kawaguchi Y. A carbon nanotube tape for serial-section electron microscopy of brain ultrastructure. Nat Commun 2018; 9:437. [PMID: 29382816 PMCID: PMC5789869 DOI: 10.1038/s41467-017-02768-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 12/26/2017] [Indexed: 01/09/2023] Open
Abstract
Automated tape-collecting ultramicrotomy in conjunction with scanning electron microscopy (SEM) is a powerful approach for volume electron microscopy and three-dimensional neuronal circuit analysis. Current tapes are limited by section wrinkle formation, surface scratches and sample charging during imaging. Here we show that a plasma-hydrophilized carbon nanotube (CNT)-coated polyethylene terephthalate (PET) tape effectively resolves these issues and produces SEM images of comparable quality to those from transmission electron microscopy. CNT tape can withstand multiple rounds of imaging, offer low surface resistance across the entire tape length and generate no wrinkles during the collection of ultrathin sections. When combined with an enhanced en bloc staining protocol, CNT tape-processed brain sections reveal detailed synaptic ultrastructure. In addition, CNT tape is compatible with post-embedding immunostaining for light and electron microscopy. We conclude that CNT tape can enable high-resolution volume electron microscopy for brain ultrastructure analysis.
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Affiliation(s)
- Yoshiyuki Kubota
- Division of Cerebral Circuitry, National Institute for Physiological Sciences, 5-1 Myodaiji-Higashiyama, Okazaki, Aichi, 444-8787, Japan. .,Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), 5-1 Myodaiji-Higashiyama, Okazaki, Aichi, 444-8787, Japan.
| | - Jaerin Sohn
- Division of Cerebral Circuitry, National Institute for Physiological Sciences, 5-1 Myodaiji-Higashiyama, Okazaki, Aichi, 444-8787, Japan.,Research Fellow of Japan Society for the Promotion of Science (JSPS), 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan
| | - Sayuri Hatada
- Division of Cerebral Circuitry, National Institute for Physiological Sciences, 5-1 Myodaiji-Higashiyama, Okazaki, Aichi, 444-8787, Japan
| | - Meike Schurr
- Department of Connectomics, Max-Planck Institute for Brain Research, Max-von-Laue-Str. 4, D-60438, Frankfurt, Germany
| | - Jakob Straehle
- Department of Connectomics, Max-Planck Institute for Brain Research, Max-von-Laue-Str. 4, D-60438, Frankfurt, Germany
| | - Anjali Gour
- Department of Connectomics, Max-Planck Institute for Brain Research, Max-von-Laue-Str. 4, D-60438, Frankfurt, Germany
| | - Ralph Neujahr
- Carl Zeiss Microscopy GmbH, ZEISS Microscopy Customer Center Europe, Rudolph-Eber-Str. 2, D- 873447, Oberkochen, Germany
| | - Takafumi Miki
- Graduate School of Brain Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0394, Japan
| | - Shawn Mikula
- Electrons-Photons-Neurons, Max-Planck Institute of Neurobiology, Am Klopferspitz 18, D-82152, Martinsried, Germany
| | - Yasuo Kawaguchi
- Division of Cerebral Circuitry, National Institute for Physiological Sciences, 5-1 Myodaiji-Higashiyama, Okazaki, Aichi, 444-8787, Japan.,Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), 5-1 Myodaiji-Higashiyama, Okazaki, Aichi, 444-8787, Japan
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22
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Vöcking O, Kourtesis I, Tumu SC, Hausen H. Co-expression of xenopsin and rhabdomeric opsin in photoreceptors bearing microvilli and cilia. eLife 2017; 6:23435. [PMID: 28876222 PMCID: PMC5648526 DOI: 10.7554/elife.23435] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 09/01/2017] [Indexed: 12/22/2022] Open
Abstract
Ciliary and rhabdomeric opsins are employed by different kinds of photoreceptor cells, such as ciliary vertebrate rods and cones or protostome microvillar eye photoreceptors, that have specialized structures and molecular physiologies. We report unprecedented cellular co-expression of rhabdomeric opsin and a visual pigment of the recently described xenopsins in larval eyes of a mollusk. The photoreceptors bear both microvilli and cilia and express proteins that are orthologous to transporters in microvillar and ciliary opsin trafficking. Highly conserved but distinct gene structures suggest that xenopsins and ciliary opsins are of independent origin, irrespective of their mutually exclusive distribution in animals. Furthermore, we propose that frequent opsin gene loss had a large influence on the evolution, organization and function of brain and eye photoreceptor cells in bilaterian animals. The presence of xenopsin in eyes of even different design might be due to a common origin and initial employment of this protein in a highly plastic photoreceptor cell type of mixed microvillar/ciliary organization. Animal eyes have photoreceptor cells that contain light-sensitive molecules called opsins. Although all animal photoreceptor cells of this kind share a common origin, the cells found in different organisms can differ considerably. The photoreceptor cells in flies, squids and other invertebrates store a type of opsin called r-opsin in thin projections on the surface known as microvilli. On the other hand, the visual photoreceptor cells in human and other vertebrate eyes transport another type of opsin (known as c-opsin) into more prominent extensions called cilia. It has been suggested that the fly and vertebrate photoreceptor cells represent clearly distinct evolutionary lineages of cells, which diverged early in animal evolution. However, several organisms that are more closely related to flies than to vertebrates have eye photoreceptor cells with cilia. Do all eye photoreceptors with cilia have a common origin in evolution or did they emerge independently in vertebrates and certain invertebrates? The photoreceptor cells of a marine mollusc called Leptochiton asellus, are unusual because they bear both microvilli and cilia, suggesting they have intermediate characteristics between the two well-known types of photoreceptor cells. Previous studies have shown that these photoreceptor cells use r-opsin, but Vöcking et al. have now detected the presence of an additional opsin in the cells. This opsin is a member of the recently discovered xenopsin family of molecules. Further analyses support the findings of previous studies that suggested this type of opsin emerged early on in animal evolution, independently from c-opsin. Other invertebrates that have cilia on their eye photoreceptors also use xenopsin and not c-opsin. The findings of Vöcking et al. suggest that, in addition to c-opsin and r-opsin, xenopsin has also driven the evolution of photoreceptor cells in animals. Eye photoreceptor cells in invertebrates with cilia probably share a common origin with the microvilli photoreceptor cells that is distinct from that of vertebrate visual cells. The observation that two very different types of opsin can be produced within a single cell suggests that the molecular processes that respond to light in photoreceptor cells may be much more complex than previously anticipated. Further work on these processes may help us to understand how animal eyes work and how they are affected by disease.
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Affiliation(s)
- Oliver Vöcking
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.,Department of Ophthalmology, University of Pittsburgh, Pittsburgh, United States
| | - Ioannis Kourtesis
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Sharat Chandra Tumu
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Harald Hausen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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23
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Ng J, Browning A, Lechner L, Terada M, Howard G, Jefferis GSXE. Genetically targeted 3D visualisation of Drosophila neurons under Electron Microscopy and X-Ray Microscopy using miniSOG. Sci Rep 2016; 6:38863. [PMID: 27958322 PMCID: PMC5153665 DOI: 10.1038/srep38863] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/11/2016] [Indexed: 11/23/2022] Open
Abstract
Large dimension, high-resolution imaging is important for neural circuit visualisation as neurons have both long- and short-range patterns: from axons and dendrites to the numerous synapses at terminal endings. Electron Microscopy (EM) is the favoured approach for synaptic resolution imaging but how such structures can be segmented from high-density images within large volume datasets remains challenging. Fluorescent probes are widely used to localise synapses, identify cell-types and in tracing studies. The equivalent EM approach would benefit visualising such labelled structures from within sub-cellular, cellular, tissue and neuroanatomical contexts. Here we developed genetically-encoded, electron-dense markers using miniSOG. We demonstrate their ability in 1) labelling cellular sub-compartments of genetically-targeted neurons, 2) generating contrast under different EM modalities, and 3) segmenting labelled structures from EM volumes using computer-assisted strategies. We also tested non-destructive X-ray imaging on whole Drosophila brains to evaluate contrast staining. This enabled us to target specific regions for EM volume acquisition.
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Affiliation(s)
- Julian Ng
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ, United Kingdom.,Neurobiology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH, United Kingdom
| | - Alyssa Browning
- Carl Zeiss X-ray Microscopy Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
| | - Lorenz Lechner
- Carl Zeiss X-ray Microscopy Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
| | - Masako Terada
- Carl Zeiss X-ray Microscopy Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
| | - Gillian Howard
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH, United Kingdom
| | - Gregory S X E Jefferis
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ, United Kingdom.,Neurobiology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH, United Kingdom
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24
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Begemann I, Galic M. Correlative Light Electron Microscopy: Connecting Synaptic Structure and Function. Front Synaptic Neurosci 2016; 8:28. [PMID: 27601992 PMCID: PMC4993758 DOI: 10.3389/fnsyn.2016.00028] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/12/2016] [Indexed: 11/20/2022] Open
Abstract
Many core paradigms of contemporary neuroscience are based on information obtained by electron or light microscopy. Intriguingly, these two imaging techniques are often viewed as complementary, yet separate entities. Recent technological advancements in microscopy techniques, labeling tools, and fixation or preparation procedures have fueled the development of a series of hybrid approaches that allow correlating functional fluorescence microscopy data and ultrastructural information from electron micrographs from a singular biological event. As correlative light electron microscopy (CLEM) approaches become increasingly accessible, long-standing neurobiological questions regarding structure-function relation are being revisited. In this review, we will survey what developments in electron and light microscopy have spurred the advent of correlative approaches, highlight the most relevant CLEM techniques that are currently available, and discuss its potential and limitations with respect to neuronal and synapse-specific applications.
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Affiliation(s)
- Isabell Begemann
- DFG Cluster of Excellence 'Cells in Motion', (EXC 1003), University of Muenster, MuensterGermany; Institute of Medical Physics and Biophysics, University Hospital Münster, University of Muenster, MuensterGermany
| | - Milos Galic
- DFG Cluster of Excellence 'Cells in Motion', (EXC 1003), University of Muenster, MuensterGermany; Institute of Medical Physics and Biophysics, University Hospital Münster, University of Muenster, MuensterGermany
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25
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Bourne JN, Schoppa NE. Three-dimensional synaptic analyses of mitral cell and external tufted cell dendrites in rat olfactory bulb glomeruli. J Comp Neurol 2016; 525:592-609. [PMID: 27490056 DOI: 10.1002/cne.24089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/13/2016] [Accepted: 07/28/2016] [Indexed: 11/07/2022]
Abstract
Recent studies have suggested that the two excitatory cell classes of the mammalian olfactory bulb, the mitral cells (MCs) and tufted cells (TCs), differ markedly in physiological responses. For example, TCs are more sensitive and broadly tuned to odors than MCs and also are much more sensitive to stimulation of olfactory sensory neurons (OSNs) in bulb slices. To examine the morphological bases for these differences, we performed quantitative ultrastructural analyses of glomeruli in rat olfactory bulb under conditions in which specific cells were labeled with biocytin and 3,3'-diaminobenzidine. Comparisons were made between MCs and external TCs (eTCs), which are a TC subtype in the glomerular layer with large, direct OSN signals and capable of mediating feedforward excitation of MCs. Three-dimensional analysis of labeled apical dendrites under an electron microscope revealed that MCs and eTCs in fact have similar densities of several chemical synapse types, including OSN inputs. OSN synapses also were distributed similarly, favoring a distal localization on both cells. Analysis of unlabeled putative MC dendrites further revealed gap junctions distributed uniformly along the apical dendrite and, on average, proximally with respect to OSN synapses. Our results suggest that the greater sensitivity of eTCs vs. MCs is due not to OSN synapse number or absolute location but rather to a conductance in the MC dendrite that is well positioned to attenuate excitatory signals passing to the cell soma. Functionally, such a mechanism could allow rapid and dynamic control of OSN-driven action potential firing in MCs through changes in gap junction properties. J. Comp. Neurol. 525:592-609, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jennifer N Bourne
- Department of Physiology and Biophysics, University of Colorado School of Medicine, Aurora, Colorado, 80045
| | - Nathan E Schoppa
- Department of Physiology and Biophysics, University of Colorado School of Medicine, Aurora, Colorado, 80045.,Neuroscience Program, University of Colorado School of Medicine, Aurora, Colorado, 80045
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Holm J, Keller RR. Angularly-selective transmission imaging in a scanning electron microscope. Ultramicroscopy 2016; 167:43-56. [DOI: 10.1016/j.ultramic.2016.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/27/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
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Kuipers J, Kalicharan RD, Wolters AHG, van Ham TJ, Giepmans BNG. Large-scale Scanning Transmission Electron Microscopy (Nanotomy) of Healthy and Injured Zebrafish Brain. J Vis Exp 2016. [PMID: 27285162 PMCID: PMC4927742 DOI: 10.3791/53635] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Large-scale 2D electron microscopy (EM), or nanotomy, is the tissue-wide application of nanoscale resolution electron microscopy. Others and we previously applied large scale EM to human skin pancreatic islets, tissue culture and whole zebrafish larvae1-7. Here we describe a universally applicable method for tissue-scale scanning EM for unbiased detection of sub-cellular and molecular features. Nanotomy was applied to investigate the healthy and a neurodegenerative zebrafish brain. Our method is based on standardized EM sample preparation protocols: Fixation with glutaraldehyde and osmium, followed by epoxy-resin embedding, ultrathin sectioning and mounting of ultrathin-sections on one-hole grids, followed by post staining with uranyl and lead. Large-scale 2D EM mosaic images are acquired using a scanning EM connected to an external large area scan generator using scanning transmission EM (STEM). Large scale EM images are typically ~ 5 - 50 G pixels in size, and best viewed using zoomable HTML files, which can be opened in any web browser, similar to online geographical HTML maps. This method can be applied to (human) tissue, cross sections of whole animals as well as tissue culture1-5. Here, zebrafish brains were analyzed in a non-invasive neuronal ablation model. We visualize within a single dataset tissue, cellular and subcellular changes which can be quantified in various cell types including neurons and microglia, the brain's macrophages. In addition, nanotomy facilitates the correlation of EM with light microscopy (CLEM)8 on the same tissue, as large surface areas previously imaged using fluorescent microscopy, can subsequently be subjected to large area EM, resulting in the nano-anatomy (nanotomy) of tissues. In all, nanotomy allows unbiased detection of features at EM level in a tissue-wide quantifiable manner.
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Naugle MM, Lozano SA, Guarraci FA, Lindsey LF, Kim JE, Morrison JH, Janssen WG, Yin W, Gore AC. Age and Long-Term Hormone Treatment Effects on the Ultrastructural Morphology of the Median Eminence of Female Rhesus Macaques. Neuroendocrinology 2016; 103:650-64. [PMID: 26536204 PMCID: PMC4860175 DOI: 10.1159/000442015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 10/29/2015] [Indexed: 12/26/2022]
Abstract
The median eminence (ME) of the hypothalamus comprises the hypothalamic nerve terminals, glia (especially tanycytes) and the portal capillary vasculature that transports hypothalamic neurohormones to the anterior pituitary gland. The ultrastructure of the ME is dynamically regulated by hormones and undergoes organizational changes during development and reproductive cycles in adult females, but relatively little is known about the ME during aging, especially in nonhuman primates. Therefore, we used a novel transmission scanning electron microscopy technique to examine the cytoarchitecture of the ME of young and aged female rhesus macaques in a preclinical monkey model of menopausal hormone treatments. Rhesus macaques were ovariectomized and treated for 2 years with vehicle, estradiol (E2), or estradiol + progesterone (E2 + P4). While the overall cytoarchitecture of the ME underwent relatively few changes with age and hormones, changes to some features of neural and glial components near the portal capillaries were observed. Specifically, large neuroterminal size was greater in aged compared to young adult animals, an effect that was mitigated or reversed by E2 alone but not by E2 + P4 treatment. Overall glial size and the density and tissue fraction of the largest subset of glia were greater in aged monkeys, and in some cases reversed by E2 treatment. Mitochondrial size was decreased by E2, but not E2 + P4, only in aged macaques. These results contrast substantially with work in rodents, suggesting that the ME of aging macaques is less vulnerable to age-related disorganization, and that the effects of E2 on monkeys' ME are age specific.
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Affiliation(s)
| | - Sateria A. Lozano
- Division of Pharmacology & Toxicology, University of Texas at Austin, Austin, TX
| | - Fay A. Guarraci
- Department of Psychology, Southwestern University, Georgetown, TX
| | - Larry F. Lindsey
- Center for Learning and Memory, University of Texas at Austin, Austin, TX
| | - Ji E. Kim
- Division of Pharmacology & Toxicology, University of Texas at Austin, Austin, TX
| | - John H. Morrison
- Fishberg Department of Neuroscience and the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - William G.M. Janssen
- Fishberg Department of Neuroscience and the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Weiling Yin
- Division of Pharmacology & Toxicology, University of Texas at Austin, Austin, TX
| | - Andrea C. Gore
- Institute for Neuroscience, University of Texas at Austin, Austin, TX
- Division of Pharmacology & Toxicology, University of Texas at Austin, Austin, TX
- Institute for Cellular & Molecular Biology, University of Texas at Austin, Austin, TX
- Correspondence: Andrea C Gore, PhD, The University of Texas at Austin, 107 West Dean Keeton, C0875, Austin, TX, 78712, USA, ; Tel: +1-512-471-3669; Fax: +1-512-471-5002
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Vöcking O, Kourtesis I, Hausen H. Posterior eyespots in larval chitons have a molecular identity similar to anterior cerebral eyes in other bilaterians. EvoDevo 2015; 6:40. [PMID: 26702352 PMCID: PMC4689004 DOI: 10.1186/s13227-015-0036-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/19/2015] [Indexed: 11/17/2022] Open
Abstract
Background Development of cerebral eyes is generally based on fine-tuned networks and closely intertwined with the formation of brain and head. Consistently and best studied in insects and vertebrates, many signaling pathways relaying the activity of eye developmental factors to positional information in the head region are characterized. Though known from several organisms, photoreceptors developing outside the head region are much less studied and the course of their development, relation to cerebral eyes and evolutionary origin is in most cases unknown. To explore how position influences development of otherwise similar photoreceptors, we analyzed the molecular characteristics of photoreceptors we discovered at the very anterior, the posttrochal mid-body and posterior body region of larval Leptochiton asellus, a representative of the chiton subgroup of mollusks. Results Irrespective of their position, all found photoreceptors exhibit a molecular signature highly similar to cerebral eye photoreceptors of related animals. All photoreceptors employ the same subtype of visual pigments (r-opsin), and the same key elements for phototransduction such as GNAq, trpC and arrestin and intracellular r-opsin transport such as rip11 and myosinV as described from other protostome cerebral eyes. Several transcription factors commonly involved in cerebral eye and brain development such as six1/2, eya, dachshund, lhx2/9 and prox are also expressed by all found photoreceptor cells, only pax6 being restricted to the anterior most cells. Coexpression of pax6 and MITF in photoreceptor-associated shielding pigment cells present at the mid-body position matches the common situation in cerebral eye retinal pigment epithelium specification and differentiation. Notably, all photoreceptors, even the posterior ones, further express clear anterior markers such as foxq2, irx, otx, and six3/6 (only the latter absent in the most posterior photoreceptors), which play important roles in the early patterning of the anterior neurogenic area throughout the animal kingdom. Conclusions Our data suggest that anterior eyes with brain-associated development can indeed be subject to heterotopic replication to developmentally distinct and even posterior body regions. Retention of the transcriptional activity of a broad set of eye developmental factors and common anterior markers suggests a mode of eye development induction, which is largely independent of body regionalization. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0036-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oliver Vöcking
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway ; Department of Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Ioannis Kourtesis
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Harald Hausen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
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Treweek JB, Chan KY, Flytzanis NC, Yang B, Deverman BE, Greenbaum A, Lignell A, Xiao C, Cai L, Ladinsky MS, Bjorkman PJ, Fowlkes CC, Gradinaru V. Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. Nat Protoc 2015; 10:1860-1896. [PMID: 26492141 PMCID: PMC4917295 DOI: 10.1038/nprot.2015.122] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1-2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks.
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Affiliation(s)
- Jennifer B Treweek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Ken Y Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Nicholas C Flytzanis
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Bin Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Benjamin E Deverman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Alon Greenbaum
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Antti Lignell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Cheng Xiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Long Cai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Charless C Fowlkes
- Department of Computer Science, University of California, Irvine, California, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
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31
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Harris KM, Spacek J, Bell ME, Parker PH, Lindsey LF, Baden AD, Vogelstein JT, Burns R. A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development. Sci Data 2015; 2:150046. [PMID: 26347348 PMCID: PMC4555877 DOI: 10.1038/sdata.2015.46] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/12/2015] [Indexed: 12/29/2022] Open
Abstract
Resurgent interest in synaptic circuitry and plasticity has emphasized the importance of 3D reconstruction from serial section electron microscopy (3DEM). Three volumes of hippocampal CA1 neuropil from adult rat were imaged at X-Y resolution of ~2 nm on serial sections of ~50-60 nm thickness. These are the first densely reconstructed hippocampal volumes. All axons, dendrites, glia, and synapses were reconstructed in a cube (~10 μm(3)) surrounding a large dendritic spine, a cylinder (~43 μm(3)) surrounding an oblique dendritic segment (3.4 μm long), and a parallelepiped (~178 μm(3)) surrounding an apical dendritic segment (4.9 μm long). The data provide standards for identifying ultrastructural objects in 3DEM, realistic reconstructions for modeling biophysical properties of synaptic transmission, and a test bed for enhancing reconstruction tools. Representative synapses are quantified from varying section planes, and microtubules, polyribosomes, smooth endoplasmic reticulum, and endosomes are identified and reconstructed in a subset of dendrites. The original images, traces, and Reconstruct software and files are freely available and visualized at the Open Connectome Project (Data Citation 1).
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Affiliation(s)
- Kristen M Harris
- Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, 1 University Station C7000 , Austin, Texas 78712, USA
| | - Josef Spacek
- Department of Pathology, Charles University at Prague, Faculty of Medicine , 500 35 Hradec Kralove, Czech Republic
| | - Maria Elizabeth Bell
- Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, 1 University Station C7000 , Austin, Texas 78712, USA
| | - Patrick H Parker
- Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, 1 University Station C7000 , Austin, Texas 78712, USA
| | - Laurence F Lindsey
- Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, 1 University Station C7000 , Austin, Texas 78712, USA
| | - Alexander D Baden
- Department of Computer Science, Institute for Data Intensive Science and Engineering, Johns Hopkins University, 160 Malone Hall, 3400 N. Charles St. , Baltimore, Maryland 21218, USA
| | - Joshua T Vogelstein
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Clark Hall Room 317C, 3400 N. Charles St. , Baltimore, Maryland 21218, USA
| | - Randal Burns
- Department of Computer Science, Institute for Data Intensive Science and Engineering, Johns Hopkins University, 160 Malone Hall, 3400 N. Charles St. , Baltimore, Maryland 21218, USA
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32
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de Boer P, Hoogenboom JP, Giepmans BNG. Correlated light and electron microscopy: ultrastructure lights up! Nat Methods 2015; 12:503-13. [PMID: 26020503 DOI: 10.1038/nmeth.3400] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 04/15/2015] [Indexed: 12/15/2022]
Abstract
Microscopy has gone hand in hand with the study of living systems since van Leeuwenhoek observed living microorganisms and cells in 1674 using his light microscope. A spectrum of dyes and probes now enable the localization of molecules of interest within living cells by fluorescence microscopy. With electron microscopy (EM), cellular ultrastructure has been revealed. Bridging these two modalities, correlated light microscopy and EM (CLEM) opens new avenues. Studies of protein dynamics with fluorescent proteins (FPs), which leave the investigator 'in the dark' concerning cellular context, can be followed by EM examination. Rare events can be preselected at the light microscopy level before EM analysis. Ongoing development-including of dedicated probes, integrated microscopes, large-scale and three-dimensional EM and super-resolution fluorescence microscopy-now paves the way for broad CLEM implementation in biology.
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Affiliation(s)
- Pascal de Boer
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jacob P Hoogenboom
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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33
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Kuipers J, de Boer P, Giepmans BNG. Scanning EM of non-heavy metal stained biosamples: Large-field of view, high contrast and highly efficient immunolabeling. Exp Cell Res 2015; 337:202-7. [PMID: 26272543 DOI: 10.1016/j.yexcr.2015.07.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022]
Abstract
Scanning electron microscopy (SEM) is increasing its application in life sciences for electron density measurements of ultrathin sections. These are traditionally analyzed with transmission electron microscopy (TEM); by most labs, SEM analysis still is associated with surface imaging only. Here we report several advantages of SEM for thin sections over TEM, both for structural inspection, as well as analyzing immuno-targeted labels such as quantum dots (QDs) and gold, where we find that QD-labeling is ten times more efficient than gold-labeling. Furthermore, we find that omitting post-staining with uranyl and lead leads to QDs readily detectable over the ultrastructure, but under these conditions ultrastructural contrast was even almost invisible in TEM examination. Importantly, imaging in SEM with STEM detection leads to both outstanding QDs and ultrastructural contrast. STEM imaging is superior over back-scattered electron imaging of these non-contrasted samples, whereas secondary electron detection cannot be used at all. We conclude that examination of ultrathin sections by SEM, which may be immunolabeled with QDs, will allow rapid and straightforward analysis of large fields with more efficient labeling than can be achieved with immunogold. The large fields of view routinely achieved with SEM, but not with TEM, allows straightforward raw data sharing using virtual microscopy, also known as nanotomy when this concerns EM data in the life sciences.
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Affiliation(s)
- Jeroen Kuipers
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Pascal de Boer
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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Kuipers J, van Ham TJ, Kalicharan RD, Veenstra-Algra A, Sjollema KA, Dijk F, Schnell U, Giepmans BNG. FLIPPER, a combinatorial probe for correlated live imaging and electron microscopy, allows identification and quantitative analysis of various cells and organelles. Cell Tissue Res 2015; 360:61-70. [PMID: 25786736 PMCID: PMC4379394 DOI: 10.1007/s00441-015-2142-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/30/2015] [Indexed: 11/25/2022]
Abstract
Ultrastructural examination of cells and tissues by electron microscopy (EM) yields detailed information on subcellular structures. However, EM is typically restricted to small fields of view at high magnification; this makes quantifying events in multiple large-area sample sections extremely difficult. Even when combining light microscopy (LM) with EM (correlated LM and EM: CLEM) to find areas of interest, the labeling of molecules is still a challenge. We present a new genetically encoded probe for CLEM, named "FLIPPER", which facilitates quantitative analysis of ultrastructural features in cells. FLIPPER consists of a fluorescent protein (cyan, green, orange, or red) for LM visualization, fused to a peroxidase allowing visualization of targets at the EM level. The use of FLIPPER is straightforward and because the module is completely genetically encoded, cells can be optimally prepared for EM examination. We use FLIPPER to quantify cellular morphology at the EM level in cells expressing a normal and disease-causing point-mutant cell-surface protein called EpCAM (epithelial cell adhesion molecule). The mutant protein is retained in the endoplasmic reticulum (ER) and could therefore alter ER function and morphology. To reveal possible ER alterations, cells were co-transfected with color-coded full-length or mutant EpCAM and a FLIPPER targeted to the ER. CLEM examination of the mixed cell population allowed color-based cell identification, followed by an unbiased quantitative analysis of the ER ultrastructure by EM. Thus, FLIPPER combines bright fluorescent proteins optimized for live imaging with high sensitivity for EM labeling, thereby representing a promising tool for CLEM.
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Affiliation(s)
- Jeroen Kuipers
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Tjakko J. van Ham
- Present Address: Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ruby D. Kalicharan
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Anneke Veenstra-Algra
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Klaas A. Sjollema
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Freark Dijk
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ulrike Schnell
- Present Address: Department of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, Dallas, Tex. USA
| | - Ben N. G. Giepmans
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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35
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Sokol E, Kramer D, Diercks GFH, Kuipers J, Jonkman MF, Pas HH, Giepmans BNG. Large-Scale Electron Microscopy Maps of Patient Skin and Mucosa Provide Insight into Pathogenesis of Blistering Diseases. J Invest Dermatol 2015; 135:1763-1770. [PMID: 25789704 DOI: 10.1038/jid.2015.109] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/23/2015] [Accepted: 02/03/2015] [Indexed: 12/24/2022]
Abstract
Large-scale electron microscopy ("nanotomy") allows straight forward ultrastructural examination of tissue, cells, organelles, and macromolecules in a single data set. Such data set equals thousands of conventional electron microscopy images and is freely accessible (www.nanotomy.org). The software allows zooming in and out of the image from total overview to nanometer scale resolution in a 'Google Earth' approach. We studied the life-threatening human autoimmune blistering disease pemphigus, using nanotomy. The pathomechanism of cell-cell separation (acantholysis) that underlies the blistering is poorly understood. Ultrastructural examination of pemphigus tissue revealed previously unreported findings: (i) the presence of double-membrane structures between cells in all pemphigus types; (ii) the absence of desmosomes around spontaneous blisters in pemphigus foliaceus (PF); (iii) lower level blistering in PF when force induced; and (iv) intercellular widening at non-acantholytic cell layers. Thus, nanotomy delivers open-source electron microscopic maps of patient tissue, which can be analyzed for additional anomalies from any computer by experts from different fields.
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Affiliation(s)
- Ena Sokol
- Department of Cell Biology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands; Department of Dermatology, Center for Blistering Diseases, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Duco Kramer
- Department of Dermatology, Center for Blistering Diseases, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Gilles F H Diercks
- Department of Dermatology, Center for Blistering Diseases, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Jeroen Kuipers
- Department of Cell Biology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Marcel F Jonkman
- Department of Dermatology, Center for Blistering Diseases, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Hendri H Pas
- Department of Dermatology, Center for Blistering Diseases, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands.
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36
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Kaynig V, Vazquez-Reina A, Knowles-Barley S, Roberts M, Jones TR, Kasthuri N, Miller E, Lichtman J, Pfister H. Large-scale automatic reconstruction of neuronal processes from electron microscopy images. Med Image Anal 2015; 22:77-88. [PMID: 25791436 DOI: 10.1016/j.media.2015.02.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 11/02/2014] [Accepted: 02/06/2015] [Indexed: 01/14/2023]
Abstract
Automated sample preparation and electron microscopy enables acquisition of very large image data sets. These technical advances are of special importance to the field of neuroanatomy, as 3D reconstructions of neuronal processes at the nm scale can provide new insight into the fine grained structure of the brain. Segmentation of large-scale electron microscopy data is the main bottleneck in the analysis of these data sets. In this paper we present a pipeline that provides state-of-the art reconstruction performance while scaling to data sets in the GB-TB range. First, we train a random forest classifier on interactive sparse user annotations. The classifier output is combined with an anisotropic smoothing prior in a Conditional Random Field framework to generate multiple segmentation hypotheses per image. These segmentations are then combined into geometrically consistent 3D objects by segmentation fusion. We provide qualitative and quantitative evaluation of the automatic segmentation and demonstrate large-scale 3D reconstructions of neuronal processes from a 27,000 μm(3) volume of brain tissue over a cube of 30 μm in each dimension corresponding to 1000 consecutive image sections. We also introduce Mojo, a proofreading tool including semi-automated correction of merge errors based on sparse user scribbles.
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Affiliation(s)
- Verena Kaynig
- School of Engineering and Applied Sciences, Harvard University, United States
| | - Amelio Vazquez-Reina
- School of Engineering and Applied Sciences, Harvard University, United States; Department of Computer Science at Tufts University, United States
| | | | - Mike Roberts
- School of Engineering and Applied Sciences, Harvard University, United States
| | - Thouis R Jones
- School of Engineering and Applied Sciences, Harvard University, United States; Department of Molecular and Cellular Biology, Harvard University, United States
| | - Narayanan Kasthuri
- Department of Molecular and Cellular Biology, Harvard University, United States
| | - Eric Miller
- Department of Computer Science at Tufts University, United States
| | - Jeff Lichtman
- Department of Molecular and Cellular Biology, Harvard University, United States
| | - Hanspeter Pfister
- School of Engineering and Applied Sciences, Harvard University, United States
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37
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Chan EM. Combinatorial approaches for developing upconverting nanomaterials: high-throughput screening, modeling, and applications. Chem Soc Rev 2015; 44:1653-79. [DOI: 10.1039/c4cs00205a] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review surveys the use of combinatorial and high-throughput techniques for the rapid discovery, optimization, and application of upconverting nanomaterials.
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Affiliation(s)
- Emory M. Chan
- The Molecular Foundry
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
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38
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Shibata S, Komaki Y, Seki F, Inouye MO, Nagai T, Okano H. Connectomics: comprehensive approaches for whole-brain mapping. Microscopy (Oxf) 2014; 64:57-67. [DOI: 10.1093/jmicro/dfu103] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Edwards J, Daniel E, Kinney J, Bartol T, Sejnowski T, Johnston D, Harris K, Bajaj C. VolRoverN: enhancing surface and volumetric reconstruction for realistic dynamical simulation of cellular and subcellular function. Neuroinformatics 2014; 12:277-89. [PMID: 24100964 DOI: 10.1007/s12021-013-9205-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Establishing meaningful relationships between cellular structure and function requires accurate morphological reconstructions. In particular, there is an unmet need for high quality surface reconstructions to model subcellular and synaptic interactions among neurons and glia at nanometer resolution. We address this need with VolRoverN, a software package that produces accurate, efficient, and automated 3D surface reconstructions from stacked 2D contour tracings. While many techniques and tools have been developed in the past for 3D visualization of cellular structure, the reconstructions from VolRoverN meet specific quality criteria that are important for dynamical simulations. These criteria include manifoldness, water-tightness, lack of self- and object-object-intersections, and geometric accuracy. These enhanced surface reconstructions are readily extensible to any cell type and are used here on spiny dendrites with complex morphology and axons from mature rat hippocampal area CA1. Both spatially realistic surface reconstructions and reduced skeletonizations are produced and formatted by VolRoverN for easy input into analysis software packages for neurophysiological simulations at multiple spatial and temporal scales ranging from ion electro-diffusion to electrical cable models.
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Affiliation(s)
- John Edwards
- Department of Computer Science, ICES, The University of Texas, Austin, TX, USA
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40
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Lucocq JM, Mayhew TM, Schwab Y, Steyer AM, Hacker C. Systems biology in 3D space--enter the morphome. Trends Cell Biol 2014; 25:59-64. [PMID: 25455351 DOI: 10.1016/j.tcb.2014.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 11/27/2022]
Abstract
Systems-based understanding of living organisms depends on acquiring huge datasets from arrays of genes, transcripts, proteins, and lipids. These data, referred to as 'omes', are assembled using 'omics' methodologies. Currently a comprehensive, quantitative view of cellular and organellar systems in 3D space at nanoscale/molecular resolution is missing. We introduce here the term 'morphome' for the distribution of living matter within a 3D biological system, and 'morphomics' for methods of collecting 3D data systematically and quantitatively. A sampling-based approach termed stereology currently provides rapid, precise, and minimally biased morphomics. We propose that stereology solves the 'big data' problem posed by emerging wide-scale electron microscopy (EM) and can establish quantitative links between the newer nanoimaging platforms such as electron tomography, cryo-EM, and correlative microscopy.
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Affiliation(s)
- John M Lucocq
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK.
| | - Terry M Mayhew
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Yannick Schwab
- Electron Microscopy Core Facility, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anna M Steyer
- Electron Microscopy Core Facility, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christian Hacker
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK
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41
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Peddie CJ, Collinson LM. Exploring the third dimension: Volume electron microscopy comes of age. Micron 2014; 61:9-19. [DOI: 10.1016/j.micron.2014.01.009] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/30/2014] [Accepted: 01/30/2014] [Indexed: 12/12/2022]
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