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Nossar LF, Lopes JA, Pereira-Acácio A, Costa-Sarmento G, Rachid R, Wendt CHC, Miranda K, Galina A, Rodrigues-Ferreira C, Muzi-Filho H, Vieyra A. Chronic undernutrition impairs renal mitochondrial respiration accompanied by intense ultrastructural damage in juvenile rats. Biochem Biophys Res Commun 2024; 739:150583. [PMID: 39182354 DOI: 10.1016/j.bbrc.2024.150583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/08/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
This study investigated whether chronic undernutrition alters the mitochondrial structure and function in renal proximal tubule cells, thus impairing fluid transport and homeostasis. We previously showed that chronic undernutrition downregulates the renal proximal tubules (Na++K+)ATPase, the main molecular machine responsible for fluid transport and ATP consumption. Male rats received a multifactorial deficient diet, the so-called Regional Basic Diet (RBD), mimicking those used in impoverished regions worldwide, from weaning to a juvenile age (3 months). The diet has a low content (8 %) of poor-quality proteins, low lipids, and no vitamins compared to control (CTR). We investigated citrate synthase activity, mitochondrial respiration (oxygraphy) in phosphorylating and non-phosphorylating conditions with different substrates/inhibitors, potential across the internal membrane (Δψ), and anion superoxide/H2O2 formation. The data were correlated with ultrastructural alterations evaluated using transmission electron microscopy (TEM) and focused ion beam scanning electron microscopy (FIB-SEM). Citrate synthase activity decreased (∼50 %) in RBD rats, accompanied by a similar reduction in respiration in non-phosphorylating conditions, maximum respiratory capacity, and ATP synthesis. The Δψ generation and its dissipation after carbonyl cyanide-4-(trifluoromethoxy) phenylhydrazone remained unmodified in the survival mitochondria. H2O2 production increased (∼100 %) after Complex II energization. TEM demonstrated intense matrix vacuolization and disruption of cristae junctions in a subpopulation of RBD mitochondria, which was also demonstrated in the 3D analysis of FIB-SEM tomography. In conclusion, chronic undernutrition impairs mitochondrial functions in renal proximal tubules, with profound alterations in the matrix and internal membrane ultrastructure that culminate with the compromise of ATP supply for transport processes.
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Affiliation(s)
- Luiz F Nossar
- Center for Research in Precision Medicine, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Jarlene A Lopes
- Center for Research in Precision Medicine, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; National Center of Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Amaury Pereira-Acácio
- Center for Research in Precision Medicine, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; National Center of Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; Graduate Program of Translational Biomedicine, University of Grande Rio, Duque de Caxias, 25071-202, Brazil
| | - Glória Costa-Sarmento
- Center for Research in Precision Medicine, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; National Center of Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Rachel Rachid
- Center for Research in Precision Medicine, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; National Center of Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Camila H C Wendt
- Center for Research in Precision Medicine, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; National Institute of Science and Technology for Structural Biology and Bioimaging/INBEB, Rio de Janeiro, 21941-902, Brazil
| | - Kildare Miranda
- Center for Research in Precision Medicine, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; National Center of Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; National Institute of Science and Technology for Structural Biology and Bioimaging/INBEB, Rio de Janeiro, 21941-902, Brazil
| | - Antonio Galina
- Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Clara Rodrigues-Ferreira
- Center for Research in Precision Medicine, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; National Center of Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Humberto Muzi-Filho
- Center for Research in Precision Medicine, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; National Center of Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Adalberto Vieyra
- Center for Research in Precision Medicine, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; National Center of Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil; Graduate Program of Translational Biomedicine, University of Grande Rio, Duque de Caxias, 25071-202, Brazil; National Institute of Science and Technology for Regenerative Medicine/REGENERA, Rio de Janeiro, 21941-902, Brazil.
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Wendt C, Miranda K. Endocytosis in malaria parasites: An ultrastructural perspective of membrane interplay in a unique infection model. CURRENT TOPICS IN MEMBRANES 2024; 93:27-49. [PMID: 39181577 DOI: 10.1016/bs.ctm.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Malaria remains a major global threat, representing a severe public health problem worldwide. Annually, it is responsible for a high rate of morbidity and mortality in many tropical developing countries where the disease is endemic. The causative agent of malaria, Plasmodium spp., exhibits a complex life cycle, alternating between an invertebrate vector, which transmits the disease, and the vertebrate host. The disease pathology observed in the vertebrate host is attributed to the asexual development of Plasmodium spp. inside the erythrocyte. Once inside the red blood cell, malaria parasites cause extensive changes in the host cell, increasing membrane rigidity and altering its normal discoid shape. Additionally, during their intraerythrocytic development, malaria parasites incorporate and degrade up to 70 % of host cell hemoglobin. This mechanism is essential for parasite development and represents an important drug target. Blocking the steps related to hemoglobin endocytosis or degradation impairs parasite development and can lead to its death. The ultrastructural analysis of hemoglobin endocytosis on Plasmodium spp. has been broadly explored along the years. However, it is only recently that the proteins involved in this process have started to emerge. Here, we will review the most important features related to hemoglobin endocytosis and catabolism on malaria parasites. A special focus will be given to the recent analysis obtained through 3D visualization approaches and to the molecules involved in these mechanisms.
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Affiliation(s)
- Camila Wendt
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho and Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Laboratório de Biomineralização, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Kildare Miranda
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho and Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Zhao J, Yu X, Shentu X, Li D. The application and development of electron microscopy for three-dimensional reconstruction in life science: a review. Cell Tissue Res 2024; 396:1-18. [PMID: 38416172 DOI: 10.1007/s00441-024-03878-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/13/2024] [Indexed: 02/29/2024]
Abstract
Imaging technologies have played a pivotal role in advancing biological research by enabling visualization of biological structures and processes. While traditional electron microscopy (EM) produces two-dimensional images, emerging techniques now allow high-resolution three-dimensional (3D) characterization of specimens in situ, meeting growing needs in molecular and cellular biology. Combining transmission electron microscopy (TEM) with serial sectioning inaugurated 3D imaging, attracting biologists seeking to explore cell ultrastructure and driving advancement of 3D EM reconstruction. By comprehensively and precisely rendering internal structure and distribution, 3D TEM reconstruction provides unparalleled ultrastructural insights into cells and molecules, holding tremendous value for elucidating structure-function relationships and broadly propelling structural biology. Here, we first introduce the principle of 3D reconstruction of cells and tissues by classical approaches in TEM and then discuss modern technologies utilizing TEM and on new SEM-based as well as cryo-electron microscope (cryo-EM) techniques. 3D reconstruction techniques from serial sections, electron tomography (ET), and the recent single-particle analysis (SPA) are examined; the focused ion beam scanning electron microscopy (FIB-SEM), the serial block-face scanning electron microscopy (SBF-SEM), and automatic tape-collecting lathe ultramicrotome (ATUM-SEM) for 3D reconstruction of large volumes are discussed. Finally, we review the challenges and development prospects of these technologies in life science. It aims to provide an informative reference for biological researchers.
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Affiliation(s)
- Jingjing Zhao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Danting Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China.
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Chang S, Li L, Hong B, Liu J, Xu Y, Pang K, Zhang L, Han H, Chen X. An intelligent workflow for sub-nanoscale 3D reconstruction of intact synapses from serial section electron tomography. BMC Biol 2023; 21:198. [PMID: 37743470 PMCID: PMC10519085 DOI: 10.1186/s12915-023-01696-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND As an extension of electron tomography (ET), serial section electron tomography (serial section ET) aims to align the tomographic images of multiple thick tissue sections together, to break through the volume limitation of the single section and preserve the sub-nanoscale voxel size. It could be applied to reconstruct the intact synapse, which expands about one micrometer and contains nanoscale vesicles. However, there are several drawbacks of the existing serial section ET methods. First, locating and imaging regions of interest (ROIs) in serial sections during the shooting process is time-consuming. Second, the alignment of ET volumes is difficult due to the missing information caused by section cutting and imaging. Here we report a workflow to simplify the acquisition of ROIs in serial sections, automatically align the volume of serial section ET, and semi-automatically reconstruct the target synaptic structure. RESULTS We propose an intelligent workflow to reconstruct the intact synapse with sub-nanometer voxel size. Our workflow includes rapid localization of ROIs in serial sections, automatic alignment, restoration, assembly of serial ET volumes, and semi-automatic target structure segmentation. For the localization and acquisition of ROIs in serial sections, we use affine transformations to calculate their approximate position based on their relative location in orderly placed sections. For the alignment of consecutive ET volumes with significantly distinct appearances, we use multi-scale image feature matching and the elastic with belief propagation (BP-Elastic) algorithm to align them from coarse to fine. For the restoration of the missing information in ET, we first estimate the number of lost images based on the pixel changes of adjacent volumes after alignment. Then, we present a missing information generation network that is appropriate for small-sample of ET volume using pre-training interpolation network and distillation learning. And we use it to generate the missing information to achieve the whole volume reconstruction. For the reconstruction of synaptic ultrastructures, we use a 3D neural network to obtain them quickly. In summary, our workflow can quickly locate and acquire ROIs in serial sections, automatically align, restore, assemble serial sections, and obtain the complete segmentation result of the target structure with minimal manual manipulation. Multiple intact synapses in wild-type rat were reconstructed at a voxel size of 0.664 nm/voxel to demonstrate the effectiveness of our workflow. CONCLUSIONS Our workflow contributes to obtaining intact synaptic structures at the sub-nanometer scale through serial section ET, which contains rapid ROI locating, automatic alignment, volume reconstruction, and semi-automatic synapse reconstruction. We have open-sourced the relevant code in our workflow, so it is easy to apply it to other labs and obtain complete 3D ultrastructures which size is similar to intact synapses with sub-nanometer voxel size.
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Affiliation(s)
- Sheng Chang
- Institute of Automation, Chinese Academy of Sciences, 100190, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, 100190, Beijing, China
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Linlin Li
- Institute of Automation, Chinese Academy of Sciences, 100190, Beijing, China
| | - Bei Hong
- Institute of Automation, Chinese Academy of Sciences, 100190, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, 100190, Beijing, China
| | - Jing Liu
- Institute of Automation, Chinese Academy of Sciences, 100190, Beijing, China
| | - Yuxuan Xu
- School of Software and Microelectronics, Peking University, 100871, Beijing, China
| | - Keliang Pang
- School of Pharmaceutical Sciences, Tsinghua University, 100084, Beijing, China
| | - Lina Zhang
- Institute of Automation, Chinese Academy of Sciences, 100190, Beijing, China
| | - Hua Han
- Institute of Automation, Chinese Academy of Sciences, 100190, Beijing, China.
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Xi Chen
- Institute of Automation, Chinese Academy of Sciences, 100190, Beijing, China.
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Inoue T, Ohno N, Oishi N, Mochizuki K, Katoh R, Kondo T. Three-dimensional structural analysis of papillary thyroid carcinoma nuclei with serial block-face scanning electron microscopy (SBF-SEM). Pathol Int 2023; 73:341-350. [PMID: 37154498 DOI: 10.1111/pin.13329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/21/2023] [Indexed: 05/10/2023]
Abstract
Nuclear morphology of carcinoma cells is critical for the pathological diagnosis of papillary thyroid carcinoma (PTC). However, three-dimensional architecture of PTC nuclei is still elusive. In this study, we analyzed the three-dimensional ultrastructure of PTC nuclei using serial block-face scanning electron microscopy which takes advantage of the high-throughput acquisition of serial electron microscopic images and three-dimensional reconstruction of subcellular structures. En bloc-stained and resin-embedded specimens were prepared from surgically removed PTCs and normal thyroid tissues. We acquired two-dimensional images from serial block-face scanning electron microscopy and reconstructed three-dimensional nuclear structures. Quantitative comparisons showed that the nuclei of carcinoma cells were larger and more complex than those of normal follicular cells. The three-dimensional reconstruction of carcinoma nuclei divided intranuclear cytoplasmic inclusions into "open intranuclear cytoplasmic inclusions" connecting to cytoplasm outside the nucleus and "closed intranuclear cytoplasmic inclusions" without that connection. Cytoplasm with abundant organelles was observed in open inclusions, but closed inclusions contained fewer organelles with or without degeneration. Granules with a dense core were only observed in closed inclusions. Our observations suggested that open inclusions originate from nuclear invaginations, and disconnection from cytoplasm leads to closed inclusions.
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Affiliation(s)
- Tomohiro Inoue
- Department of Pathology, University of Yamanashi, Chuo, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, Shimotsuke, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, Japan
| | - Naoki Oishi
- Department of Pathology, University of Yamanashi, Chuo, Japan
| | - Kunio Mochizuki
- Department of Pathology, University of Yamanashi, Chuo, Japan
| | - Ryohei Katoh
- Department of Pathology, Ito Hospital, Tokyo, Japan
| | - Tetsuo Kondo
- Department of Pathology, University of Yamanashi, Chuo, Japan
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Agborbesong E, Bissler J, Li X. Liquid Biopsy at the Frontier of Kidney Diseases: Application of Exosomes in Diagnostics and Therapeutics. Genes (Basel) 2023; 14:1367. [PMID: 37510273 PMCID: PMC10379367 DOI: 10.3390/genes14071367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
In the era of precision medicine, liquid biopsy techniques, especially the use of urine analysis, represent a paradigm shift in the identification of biomarkers, with considerable implications for clinical practice in the field of nephrology. In kidney diseases, the use of this non-invasive tool to identify specific and sensitive biomarkers other than plasma creatinine and the glomerular filtration rate is becoming crucial for the diagnosis and assessment of a patient's condition. In recent years, studies have drawn attention to the importance of exosomes for diagnostic and therapeutic purposes in kidney diseases. Exosomes are nano-sized extracellular vesicles with a lipid bilayer structure, composed of a variety of biologically active substances. In the context of kidney diseases, studies have demonstrated that exosomes are valuable carriers of information and are delivery vectors, rendering them appealing candidates as biomarkers and drug delivery vehicles with beneficial therapeutic outcomes for kidney diseases. This review summarizes the applications of exosomes in kidney diseases, emphasizing the current biomarkers of renal diseases identified from urinary exosomes and the therapeutic applications of exosomes with reference to drug delivery and immunomodulation. Finally, we discuss the challenges encountered when using exosomes for therapeutic purposes and how these may affect its clinical applications.
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Affiliation(s)
- Ewud Agborbesong
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - John Bissler
- Department of Pediatrics, University of Tennessee Health Science Center and Le Bonheur Children's Hospital, Memphis, TN 38105, USA
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN 38105, USA
- Pediatric Medicine Department, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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Brunet J, Walsh CL, Wagner WL, Bellier A, Werlein C, Marussi S, Jonigk DD, Verleden SE, Ackermann M, Lee PD, Tafforeau P. Preparation of large biological samples for high-resolution, hierarchical, synchrotron phase-contrast tomography with multimodal imaging compatibility. Nat Protoc 2023; 18:1441-1461. [PMID: 36859614 DOI: 10.1038/s41596-023-00804-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/12/2022] [Indexed: 03/03/2023]
Abstract
Imaging across different scales is essential for understanding healthy organ morphology and pathophysiological changes. The macro- and microscale three-dimensional morphology of large samples, including intact human organs, is possible with X-ray microtomography (using laboratory or synchrotron sources). Preparation of large samples for high-resolution imaging, however, is challenging due to limitations such as sample shrinkage, insufficient contrast, movement of the sample and bubble formation during mounting or scanning. Here, we describe the preparation, stabilization, dehydration and mounting of large soft-tissue samples for X-ray microtomography. We detail the protocol applied to whole human organs and hierarchical phase-contrast tomography at the European Synchrotron Radiation Facility, yet it is applicable to a range of biological samples, including complete organisms. The protocol enhances the contrast when using X-ray imaging, while preventing sample motion during the scan, even with different sample orientations. Bubbles trapped during mounting and those formed during scanning (in the case of synchrotron X-ray imaging) are mitigated by multiple degassing steps. The sample preparation is also compatible with magnetic resonance imaging, computed tomography and histological observation. The sample preparation and mounting require 24-36 d for a large organ such as a whole human brain or heart. The preparation time varies depending on the composition, size and fragility of the tissue. Use of the protocol enables scanning of intact organs with a diameter of 150 mm with a local voxel size of 1 μm. The protocol requires users with expertise in handling human or animal organs, laboratory operation and X-ray imaging.
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Affiliation(s)
- J Brunet
- Department of Mechanical Engineering, University College London, London, UK.
- European Synchrotron Radiation Facility, Grenoble, France.
| | - C L Walsh
- Department of Mechanical Engineering, University College London, London, UK.
| | - W L Wagner
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Centre Heidelberg (TLRC), German Lung Research Centre (DZL), Heidelberg, Germany
| | - A Bellier
- Laboratoire d'Anatomie des Alpes Françaises (LADAF), Université Grenoble Alpes, Grenoble, France
| | - C Werlein
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - S Marussi
- Department of Mechanical Engineering, University College London, London, UK
| | - D D Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), German Lung Research Centre (DZL), Hannover, Germany
| | - S E Verleden
- Antwerp Surgical Training, Anatomy and Research Centre (ASTARC), University of Antwerp, Antwerp, Belgium
| | - M Ackermann
- Institute of Pathology and Molecular Pathology, Helios University Clinic Wuppertal, University of Witten/Herdecke, Wuppertal, Germany
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Peter D Lee
- Department of Mechanical Engineering, University College London, London, UK.
- Research Complex at Harwell, Didcot, UK.
| | - Paul Tafforeau
- European Synchrotron Radiation Facility, Grenoble, France.
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Staab-Weijnitz CA, Onursal C, Nambiar D, Vanacore R. Assessment of Collagen in Translational Models of Lung Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1413:213-244. [PMID: 37195533 DOI: 10.1007/978-3-031-26625-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The extracellular matrix (ECM) plays an important role in lung health and disease. Collagen is the main component of the lung ECM, widely used for the establishment of in vitro and organotypic models of lung disease, and as scaffold material of general interest for the field of lung bioengineering. Collagen also is the main readout for fibrotic lung disease, where collagen composition and molecular properties are drastically changed and ultimately result in dysfunctional "scarred" tissue. Because of the central role of collagen in lung disease, quantification, determination of molecular properties, and three-dimensional visualization of collagen is important for both development and characterization of translational models of lung research. In this chapter, we provide a comprehensive overview on the various methodologies currently available for quantification and characterization of collagen including their detection principles, advantages, and disadvantages.
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Affiliation(s)
- Claudia A Staab-Weijnitz
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Member of the German Center for Lung Research (DZL), Ludwig-Maximilians-Universität and Helmholtz Zentrum München, Munich, Germany.
| | - Ceylan Onursal
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Member of the German Center for Lung Research (DZL), Ludwig-Maximilians-Universität and Helmholtz Zentrum München, Munich, Germany
| | - Deepika Nambiar
- Center for Matrix Biology, Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Roberto Vanacore
- Center for Matrix Biology, Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA.
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9
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Insights from the Infection Cycle of VSV-ΔG-Spike Virus. Viruses 2022; 14:v14122828. [PMID: 36560832 PMCID: PMC9788095 DOI: 10.3390/v14122828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/20/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Fundamental key processes in viral infection cycles generally occur in distinct cellular sites where both viral and host factors accumulate and interact. These sites are usually termed viral replication organelles, or viral factories (VF). The generation of VF is accompanied by the synthesis of viral proteins and genomes and involves the reorganization of cellular structure. Recently, rVSV-ΔG-spike (VSV-S), a recombinant VSV expressing the SARS-CoV-2 spike protein, was developed as a vaccine candidate against SARS-CoV-2. By combining transmission electron microscopy (TEM) tomography studies and immuno-labeling techniques, we investigated the infection cycle of VSV-S in Vero E6 cells. RT-real-time-PCR results show that viral RNA synthesis occurs 3-4 h post infection (PI), and accumulates as the infection proceeds. By 10-24 h PI, TEM electron tomography results show that VSV-S generates VF in multi-lamellar bodies located in the cytoplasm. The VF consists of virus particles with various morphologies. We demonstrate that VSV-S infection is associated with accumulation of cytoplasmatic viral proteins co-localized with dsRNA (marker for RNA replication) but not with ER membranes. Newly formed virus particles released from the multi-lamellar bodies containing VF, concentrate in a vacuole membrane, and the infection ends with the budding of particles after the fusion of the vacuole membrane with the plasma membrane. In summary, the current study describes detailed 3D imaging of key processes during the VSV-S infection cycle.
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Rajagopal V, Pinali C, Shiels HA. New revelations on the interplay between cardiomyocyte architecture and cardiomyocyte function in growth, health, and disease: a brief introduction. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210315. [PMID: 36189809 PMCID: PMC9527918 DOI: 10.1098/rstb.2021.0315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/26/2022] Open
Affiliation(s)
- Vijay Rajagopal
- Department of Biomedical Engineering, Faculty of Engineering and IT, The University of Melbourne, Victoria 3010, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Christian Pinali
- Division of Cardiovascular Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9NT, UK
| | - Holly A. Shiels
- Division of Cardiovascular Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9NT, UK
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11
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Sengupta R, Mihelc EM, Angel S, Lanman JK, Kuhn RJ, Stahelin RV. Contribution of the Golgi apparatus in morphogenesis of a virus-induced cytopathic vacuolar system. Life Sci Alliance 2022; 5:5/10/e202000887. [PMID: 36137747 PMCID: PMC9500387 DOI: 10.26508/lsa.202000887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022] Open
Abstract
Electron tomography reveals four classes of cytopathic vesicles-II (CPV-II) stemming from the host Golgi apparatus after Venezuelan equine encephalitis virus infection. The Golgi apparatus (GA) in mammalian cells is pericentrosomally anchored and exhibits a stacked architecture. During infections by members of the alphavirus genus, the host cell GA is thought to give rise to distinct mobile pleomorphic vacuoles known as CPV-II (cytopathic vesicle-II) via unknown morphological steps. To dissect this, we adopted a phased electron tomography approach to image multiple overlapping volumes of a cell infected with Venezuelan equine encephalitis virus (VEEV) and complemented it with localization of a peroxidase-tagged Golgi marker. Analysis of the tomograms revealed a pattern of progressive cisternal bending into double-lamellar vesicles as a central process underpinning the biogenesis and the morphological complexity of this vacuolar system. Here, we propose a model for the conversion of the GA to CPV-II that reveals a unique pathway of intracellular virus envelopment. Our results have implications for alphavirus-induced displacement of Golgi cisternae to the plasma membrane to aid viral egress operating late in the infection cycle.
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Affiliation(s)
- Ranjan Sengupta
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA .,Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,The Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Elaine M Mihelc
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Stephanie Angel
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.,Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,The Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Jason K Lanman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,The Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA .,The Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
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12
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Yamane K, Oi T, Taniguchi M. Evaluation of the validity of large-scale serial sectioning TEM for three-dimensional reconstruction of rice mesophyll cells and chloroplasts. PROTOPLASMA 2022; 259:1219-1231. [PMID: 34989863 DOI: 10.1007/s00709-021-01728-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Serial sectioning transmission electron microscopy (ssTEM) is a classical method of 3D reconstruction using serial sections obtained with an ultramicrotome. However, producing a long ribbon with homogeneity is difficult. Here, ultramicrotome movement was suspended after producing a ribbon of 15-30 serial sections (cutting intervals, 100 nm), and then, the ribbon was mounted on an individual one-slot grid. However, as this ssTEM method may include influencing factors such as incorrect intervals of section thickness and distortion of sections, which is produced by cutting sections using a diamond knife and beam interaction under TEM observation, qualitative and quantitative data on rice mesophyll cells and chloroplasts were compared with those obtained from a focused ion beam scanning electron microscopy (FIB-SEM) (cutting intervals, 50 nm). No structural distortion in 3D models was observed. In addition, no significant differences in the volume and surface area were observed between the two methods. The surface to volume ratio was significantly affected by the increase in section thickness, but not the difference of methodologies. Our method was useful for observing large volumes of plant cells and organelles, leading to the identification of various sizes and types of chloroplasts. The formation of a chloroplast pocket, which is a structure surrounding other intracellular compartments, was confirmed in rice leaves grown under moderate growth conditions using the ssTEM method. As only four out of 90 chloroplasts formed pocket structures, the formation was considered to be rare under the applied moderate growth conditions.
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Affiliation(s)
- Koji Yamane
- Graduate School of Agriculture, Kindai University, Nara, 631-8505, Japan.
| | - Takao Oi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Mitsutaka Taniguchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
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13
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Huang J, Wang Z, Fan L, Ma S. A review of wheat starch analyses: Methods, techniques, structure and function. Int J Biol Macromol 2022; 203:130-142. [PMID: 35093434 DOI: 10.1016/j.ijbiomac.2022.01.149] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/28/2021] [Accepted: 01/23/2022] [Indexed: 01/31/2023]
Abstract
Wheat starch has received much attention as an important source of dietary energy for humans, an interesting carbohydrate and a polymeric material. The understanding of the structure and function of wheat starch has always been accompanied by newer technological tools. On the one hand, the general knowledge of wheat starch is constantly being enriched. On the other hand, an increasing number of studies are trying to add new insights to what is already known from two frontier perspectives, namely, wheat starch supramolecular structures and wheat starch fine structures (CLDs). This review describes the structure and function of wheat starch from the perspective of wheat starch analysis techniques (instruments).
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Affiliation(s)
- Jihong Huang
- College of Food and Medicine, Xuchang University, Xuchang, Henan 461000, China; College of Food Science and Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China.
| | - Zhen Wang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China
| | - Ling Fan
- College of Food and Medicine, Xuchang University, Xuchang, Henan 461000, China
| | - Sen Ma
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China.
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14
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Sankoh AF, Burch-Smith TM. Approaches for investigating plasmodesmata and effective communication. CURRENT OPINION IN PLANT BIOLOGY 2021; 64:102143. [PMID: 34826658 DOI: 10.1016/j.pbi.2021.102143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Plasmodesmata (PD) are integral plant cell wall components that provide routes for intercellular communication, signaling, and resource sharing. They are therefore essential for plant growth and survival. Much effort has been put forth to understand how PD are generated and their structure is refined for function and to determine how they regulate intercellular trafficking. This review provides an overview of some of the approaches that have been used to study PD structure and function, highlighting those that may be more widely adopted to address questions of PD cell biology and function. Extending our focus on the importance of communication, we address how effective communication strategies can increase diversity and accessibility in the research laboratory, focusing on challenges faced by our deaf/hard-of-hearing colleagues, and highlight successful approaches to including them in the research laboratory.
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Affiliation(s)
- Amie F Sankoh
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States
| | - Tessa M Burch-Smith
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States.
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15
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Ivanchenko MV, Indzhykulian AA, Corey DP. Electron Microscopy Techniques for Investigating Structure and Composition of Hair-Cell Stereociliary Bundles. Front Cell Dev Biol 2021; 9:744248. [PMID: 34746139 PMCID: PMC8569945 DOI: 10.3389/fcell.2021.744248] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Hair cells—the sensory cells of the vertebrate inner ear—bear at their apical surfaces a bundle of actin-filled protrusions called stereocilia, which mediate the cells’ mechanosensitivity. Hereditary deafness is often associated with morphological disorganization of stereocilia bundles, with the absence or mislocalization within stereocilia of specific proteins. Thus, stereocilia bundles are closely examined to understand most animal models of hereditary hearing loss. Because stereocilia have a diameter less than a wavelength of light, light microscopy is not adequate to reveal subtle changes in morphology or protein localization. Instead, electron microscopy (EM) has proven essential for understanding stereocilia bundle development, maintenance, normal function, and dysfunction in disease. Here we review a set of EM imaging techniques commonly used to study stereocilia, including optimal sample preparation and best imaging practices. These include conventional and immunogold transmission electron microscopy (TEM) and scanning electron microscopy (SEM), as well as focused-ion-beam scanning electron microscopy (FIB-SEM), which enables 3-D serial reconstruction of resin-embedded biological structures at a resolution of a few nanometers. Parameters for optimal sample preparation, fixation, immunogold labeling, metal coating and imaging are discussed. Special attention is given to protein localization in stereocilia using immunogold labeling. Finally, we describe the advantages and limitations of these EM techniques and their suitability for different types of studies.
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Affiliation(s)
- Maryna V Ivanchenko
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Artur A Indzhykulian
- Department of Otolaryngology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - David P Corey
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
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16
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Abstract
This review focuses on the human pancreatic islet-including its structure, cell composition, development, function, and dysfunction. After providing a historical timeline of key discoveries about human islets over the past century, we describe new research approaches and technologies that are being used to study human islets and how these are providing insight into human islet physiology and pathophysiology. We also describe changes or adaptations in human islets in response to physiologic challenges such as pregnancy, aging, and insulin resistance and discuss islet changes in human diabetes of many forms. We outline current and future interventions being developed to protect, restore, or replace human islets. The review also highlights unresolved questions about human islets and proposes areas where additional research on human islets is needed.
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Affiliation(s)
- John T Walker
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Diane C Saunders
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Marcela Brissova
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Alvin C Powers
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- VA Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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17
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Liu Z, Gao J, Cui Y, Klumpe S, Xiang Y, Erdmann PS, Jiang L. Membrane imaging in the plant endomembrane system. PLANT PHYSIOLOGY 2021; 185:562-576. [PMID: 33793889 PMCID: PMC8133680 DOI: 10.1093/plphys/kiaa040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/11/2020] [Indexed: 05/10/2023]
Abstract
Recent studies on membrane imaging in the plant endomembrane system by 2-D/3-D CLSM and TEM provide future perspectives of whole-cell ET and cryo-FIB-aided cryo-ET analysis.
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Affiliation(s)
- Zhiqi Liu
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jiayang Gao
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yong Cui
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sven Klumpe
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Yun Xiang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Philipp S Erdmann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Liwen Jiang
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
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18
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Nahirney PC, Tremblay ME. Brain Ultrastructure: Putting the Pieces Together. Front Cell Dev Biol 2021; 9:629503. [PMID: 33681208 PMCID: PMC7930431 DOI: 10.3389/fcell.2021.629503] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Unraveling the fine structure of the brain is important to provide a better understanding of its normal and abnormal functioning. Application of high-resolution electron microscopic techniques gives us an unprecedented opportunity to discern details of the brain parenchyma at nanoscale resolution, although identifying different cell types and their unique features in two-dimensional, or three-dimensional images, remains a challenge even to experts in the field. This article provides insights into how to identify the different cell types in the central nervous system, based on nuclear and cytoplasmic features, amongst other unique characteristics. From the basic distinction between neurons and their supporting cells, the glia, to differences in their subcellular compartments, organelles and their interactions, ultrastructural analyses can provide unique insights into the changes in brain function during aging and disease conditions, such as stroke, neurodegeneration, infection and trauma. Brain parenchyma is composed of a dense mixture of neuronal and glial cell bodies, together with their intertwined processes. Intracellular components that vary between cells, and can become altered with aging or disease, relate to the cytoplasmic and nucleoplasmic density, nuclear heterochromatin pattern, mitochondria, endoplasmic reticulum and Golgi complex, lysosomes, neurosecretory vesicles, and cytoskeletal elements (actin, intermediate filaments, and microtubules). Applying immunolabeling techniques to visualize membrane-bound or intracellular proteins in neurons and glial cells gives an even better appreciation of the subtle differences unique to these cells across contexts of health and disease. Together, our observations reveal how simple ultrastructural features can be used to identify specific changes in cell types, their health status, and functional relationships in the brain.
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19
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Abstract
Since its entry into biomedical research in the first half of the twentieth century, electron microscopy has been a valuable tool for lung researchers to explore the lung's delicate ultrastructure. Among others, it proved the existence of a continuous alveolar epithelium and demonstrated the surfactant lining layer. With the establishment of serial sectioning transmission electron microscopy, as the first "volume electron microscopic" technique, electron microscopy entered the third dimension and investigations of the lung's three-dimensional ultrastructure became possible. Over the years, further techniques, ranging from electron tomography over serial block-face and focused ion beam scanning electron microscopy to array tomography became available. All techniques cover different volumes and resolutions, and, thus, different scientific questions. This review gives an overview of these techniques and their application in lung research, focusing on their fields of application and practical implementation. Furthermore, an introduction is given how the output raw data are processed and the final three-dimensional models can be generated.
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Affiliation(s)
- Jan Philipp Schneider
- Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Jan Hegermann
- Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
- Research Core Unit Electron Microscopy, Hannover Medical School, 30625 Hannover, Germany
| | - Christoph Wrede
- Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
- Research Core Unit Electron Microscopy, Hannover Medical School, 30625 Hannover, Germany
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20
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Abstract
Unraveling the fine structure of the brain is important to provide a better understanding of its normal and abnormal functioning. Application of high-resolution electron microscopic techniques gives us an unprecedented opportunity to discern details of the brain parenchyma at nanoscale resolution, although identifying different cell types and their unique features in two-dimensional, or three-dimensional images, remains a challenge even to experts in the field. This article provides insights into how to identify the different cell types in the central nervous system, based on nuclear and cytoplasmic features, amongst other unique characteristics. From the basic distinction between neurons and their supporting cells, the glia, to differences in their subcellular compartments, organelles and their interactions, ultrastructural analyses can provide unique insights into the changes in brain function during aging and disease conditions, such as stroke, neurodegeneration, infection and trauma. Brain parenchyma is composed of a dense mixture of neuronal and glial cell bodies, together with their intertwined processes. Intracellular components that vary between cells, and can become altered with aging or disease, relate to the cytoplasmic and nucleoplasmic density, nuclear heterochromatin pattern, mitochondria, endoplasmic reticulum and Golgi complex, lysosomes, neurosecretory vesicles, and cytoskeletal elements (actin, intermediate filaments, and microtubules). Applying immunolabeling techniques to visualize membrane-bound or intracellular proteins in neurons and glial cells gives an even better appreciation of the subtle differences unique to these cells across contexts of health and disease. Together, our observations reveal how simple ultrastructural features can be used to identify specific changes in cell types, their health status, and functional relationships in the brain.
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Affiliation(s)
- Patrick C Nahirney
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Marie-Eve Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
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21
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Current Microscopy Strategies to Image Fungal Vesicles: From the Intracellular Trafficking and Secretion to the Inner Structure of Isolated Vesicles. Curr Top Microbiol Immunol 2021; 432:139-159. [DOI: 10.1007/978-3-030-83391-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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22
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Icick R, Forget B, Cloëz-Tayarani I, Pons S, Maskos U, Besson M. Genetic susceptibility to nicotine addiction: Advances and shortcomings in our understanding of the CHRNA5/A3/B4 gene cluster contribution. Neuropharmacology 2020; 177:108234. [PMID: 32738310 DOI: 10.1016/j.neuropharm.2020.108234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/28/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
Over the last decade, robust human genetic findings have been instrumental in elucidating the heritable basis of nicotine addiction (NA). They highlight coding and synonymous polymorphisms in a cluster on chromosome 15, encompassing the CHRNA5, CHRNA3 and CHRNB4 genes, coding for three subunits of the nicotinic acetylcholine receptor (nAChR). They have inspired an important number of preclinical studies, and will hopefully lead to the definition of novel drug targets for treating NA. Here, we review these candidate gene and genome-wide association studies (GWAS) and their direct implication in human brain function and NA-related phenotypes. We continue with a description of preclinical work in transgenic rodents that has led to a mechanistic understanding of several of the genetic hits. We also highlight important issues with regards to CHRNA3 and CHRNB4 where we are still lacking a dissection of their role in NA, including even in preclinical models. We further emphasize the use of human induced pluripotent stem cell-derived models for the analysis of synonymous and intronic variants on a human genomic background. Finally, we indicate potential avenues to further our understanding of the role of this human genetic variation. This article is part of the special issue on 'Contemporary Advances in Nicotine Neuropharmacology'.
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Affiliation(s)
- Romain Icick
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; Département de Psychiatrie et de Médecine Addictologique, Groupe Hospitalier Saint-Louis, Lariboisière, Fernand Widal, Assistance-Publique Hôpitaux de Paris, Paris, F-75010, France; INSERM UMR-S1144, Paris, F-75006, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Benoît Forget
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; Génétique Humaine et Fonctions Cognitives, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Isabelle Cloëz-Tayarani
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Stéphanie Pons
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Uwe Maskos
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Morgane Besson
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France.
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23
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Hook KA, Fisher HS. Methodological considerations for examining the relationship between sperm morphology and motility. Mol Reprod Dev 2020; 87:633-649. [PMID: 32415812 PMCID: PMC7329573 DOI: 10.1002/mrd.23346] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 04/10/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022]
Abstract
Sperm cells of all taxa share a common goal to reach and fertilize an ovum, yet sperm are one of the most diverse cell types in nature. While the structural diversity of these cells is well recognized, the functional significance of variation in sperm design remains elusive. An important function of spermatozoa is a need to migrate toward the ova, often over long distances in a foreign environment, which may include a complex and hostile female reproductive tract. Several comparative and experimental studies have attempted to address the link between sperm morphology and motility, yet the conclusions drawn from these studies are often inconsistent, even within the same taxa. Much of what we know about the functional significance of sperm design in internally fertilizing species has been gleaned from in vitro studies, for which experimental parameters often vary among studies. We propose that discordant results from these studies are in part due to a lack of consistency of methods, conditions that do not replicate those of the female reproductive tract, and the overuse of simple linear measures of sperm shape. Within this review, we provide a toolkit for imaging, quantifying, and analyzing sperm morphology and movement patterns for in vitro studies and discuss emerging approaches. Results from studies linking morphology to motility enhance our understanding of the evolution of adaptive sperm traits and the mechanisms that regulate fertility, thus offering new insights into methods used in assisted reproductive technologies in animal science, conservation and public health.
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Affiliation(s)
- Kristin A. Hook
- Department of Biology, University of Maryland, College Park, U.S.A
| | - Heidi S. Fisher
- Department of Biology, University of Maryland, College Park, U.S.A
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24
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Rozo AJ, Cox MH, Devitt A, Rothnie AJ, Goddard AD. Biophysical analysis of lipidic nanoparticles. Methods 2020; 180:45-55. [PMID: 32387313 DOI: 10.1016/j.ymeth.2020.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 12/18/2022] Open
Abstract
Biological nanoparticles include liposomes, extracellular vesicle and lipid-based discoidal systems. When studying such particles, there are several key parameters of interest, including particle size and concentration. Measuring these characteristics can be of particular importance in the research laboratory or when producing such particles as biotherapeutics. This article briefly describes the major types of lipid-containing nanoparticles and the techniques that can be used to study them. Such methodologies include electron microscopy, atomic force microscopy, dynamic light scattering, nanoparticle tracking analysis, flow cytometry, tunable resistive pulse sensing and microfluidic resistive pulse sensing. Whilst no technique is perfect for the analysis of all nanoparticles, this article provides advantages and disadvantages of each, highlighting the latest developments in the field. Finally, we demonstrate the use of microfluidic resistive pulse sensing for the analysis of biological nanoparticles.
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Affiliation(s)
- Annaïg J Rozo
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Megan H Cox
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK; Meritics Ltd, Unit 3, Clipstone Brook Industrial Estate, Cherrycourt Way, Leighton Buzzard LU7 4GP, UK
| | - Andrew Devitt
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Alice J Rothnie
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Alan D Goddard
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK.
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25
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Žerovnik Mekuč M, Bohak C, Hudoklin S, Kim BH, Romih R, Kim MY, Marolt M. Automatic segmentation of mitochondria and endolysosomes in volumetric electron microscopy data. Comput Biol Med 2020; 119:103693. [PMID: 32339123 DOI: 10.1016/j.compbiomed.2020.103693] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/11/2020] [Accepted: 02/29/2020] [Indexed: 12/26/2022]
Abstract
Automatic segmentation of intracellular compartments is a powerful technique, which provides quantitative data about presence, spatial distribution, structure and consequently the function of cells. With the recent development of high throughput volumetric data acquisition techniques in electron microscopy (EM), manual segmentation is becoming a major bottleneck of the process. To aid the cell research, we propose a technique for automatic segmentation of mitochondria and endolysosomes obtained from urinary bladder urothelial cells by the dual beam EM technique. We present a novel publicly available volumetric EM dataset - the first of urothelial cells, evaluate several state-of-the-art segmentation methods on the new dataset and present a novel segmentation pipeline, which is based on supervised deep learning and includes mechanisms that reduce the impact of dependencies in the input data, artefacts and annotation errors. We show that our approach outperforms the compared methods on the proposed dataset.
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Affiliation(s)
- Manca Žerovnik Mekuč
- Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia.
| | - Ciril Bohak
- Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia.
| | - Samo Hudoklin
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia.
| | - Byeong Hak Kim
- School of Electronics Engineering and Research Center for Neurosurgical Robotic System, Kyungpook National University, 41566 Daegu, South Korea; Hanwha Systems Corporation, Optronics Team, 1gongdan-ro, 39376 Gumi, South Korea.
| | - Rok Romih
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia.
| | - Min Young Kim
- School of Electronics Engineering and Research Center for Neurosurgical Robotic System, Kyungpook National University, 41566 Daegu, South Korea.
| | - Matija Marolt
- Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia.
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Scanning electron microscopy and machine learning reveal heterogeneity in capsular morphotypes of the human pathogen Cryptococcus spp. Sci Rep 2020; 10:2362. [PMID: 32047210 PMCID: PMC7012869 DOI: 10.1038/s41598-020-59276-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/16/2020] [Indexed: 01/09/2023] Open
Abstract
Phenotypic heterogeneity is an important trait for the development and survival of many microorganisms including the yeast Cryptococcus spp., a deadly pathogen spread worldwide. Here, we have applied scanning electron microscopy (SEM) to define four Cryptococcus spp. capsule morphotypes, namely Regular, Spiky, Bald, and Phantom. These morphotypes were persistently observed in varying proportions among yeast isolates. To assess the distribution of such morphotypes we implemented an automated pipeline capable of (1) identifying potentially cell-associated objects in the SEM-derived images; (2) computing object-level features; and (3) classifying these objects into their corresponding classes. The machine learning approach used a Random Forest (RF) classifier whose overall accuracy reached 85% on the test dataset, with per-class specificity above 90%, and sensitivity between 66 and 94%. Additionally, the RF model indicates that structural and texture features, e.g., object area, eccentricity, and contrast, are most relevant for classification. The RF results agree with the observed variation in these features, consistently also with visual inspection of SEM images. Finally, our work introduces morphological variants of Cryptococcus spp. capsule. These can be promptly identified and characterized using computational models so that future work may unveil morphological associations with yeast virulence.
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Schneider JP, Wrede C, Mühlfeld C. The Three-Dimensional Ultrastructure of the Human Alveolar Epithelium Revealed by Focused Ion Beam Electron Microscopy. Int J Mol Sci 2020; 21:ijms21031089. [PMID: 32041332 PMCID: PMC7038159 DOI: 10.3390/ijms21031089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/22/2020] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Thin type 1 alveolar epithelial (AE1) and surfactant producing type 2 alveolar epithelial (AE2) cells line the alveoli in the lung and are essential for normal lung function. Function is intimately interrelated to structure, so that detailed knowledge of the epithelial ultrastructure can significantly enhance our understanding of its function. The basolateral surface of the cells or the epithelial contact sites are of special interest, because they play an important role in intercellular communication or stabilizing the epithelium. The latter is in particular important for the lung with its variable volume. The aim of the present study was to investigate the three-dimensional (3D) ultrastructure of the human alveolar epithelium focusing on contact sites and the basolateral cell membrane of AE2 cells using focused ion beam electron microscopy and subsequent 3D reconstructions. The study provides detailed surface reconstructions of two AE1 cell domains and two AE2 cells, showing AE1/AE1, AE1/AE2 and AE2/AE2 contact sites, basolateral microvilli pits at AE2 cells and small AE1 processes beneath AE2 cells. Furthermore, we show reconstructions of a surfactant secretion pore, enlargements of the apical AE1 cell surface and long folds bordering grooves on the basal AE1 cell surface. The functional implications of our findings are discussed. These findings may lay the structural basis for further molecular investigations.
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Affiliation(s)
- Jan Philipp Schneider
- Institute of Functional and Applied Anatomy, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; (C.W.); (C.M.)
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
- Correspondence:
| | - Christoph Wrede
- Institute of Functional and Applied Anatomy, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; (C.W.); (C.M.)
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
- Research Core Unit Electron Microscopy, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Christian Mühlfeld
- Institute of Functional and Applied Anatomy, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; (C.W.); (C.M.)
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
- Research Core Unit Electron Microscopy, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
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Ranjbari E, Majdi S, Ewing A. Analytical Techniques: Shedding Light upon Nanometer-Sized Secretory Vesicles. TRENDS IN CHEMISTRY 2019. [DOI: 10.1016/j.trechm.2019.02.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Le BD, Stein JL. Mapping causal pathways from genetics to neuropsychiatric disorders using genome-wide imaging genetics: Current status and future directions. Psychiatry Clin Neurosci 2019; 73:357-369. [PMID: 30864184 PMCID: PMC6625892 DOI: 10.1111/pcn.12839] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/22/2019] [Accepted: 03/05/2019] [Indexed: 12/17/2022]
Abstract
Imaging genetics aims to identify genetic variants associated with the structure and function of the human brain. Recently, collaborative consortia have been successful in this goal, identifying and replicating common genetic variants influencing gross human brain structure as measured through magnetic resonance imaging. In this review, we contextualize imaging genetic associations as one important link in understanding the causal chain from genetic variant to increased risk for neuropsychiatric disorders. We provide examples in other fields of how identifying genetic variant associations to disease and multiple phenotypes along the causal chain has revealed a mechanistic understanding of disease risk, with implications for how imaging genetics can be similarly applied. We discuss current findings in the imaging genetics research domain, including that common genetic variants can have a slightly larger effect on brain structure than on risk for disorders like schizophrenia, indicating a somewhat simpler genetic architecture. Also, gross brain structure measurements share a genetic basis with some, but not all, neuropsychiatric disorders, invalidating the previously held belief that they are broad endophenotypes, yet pinpointing brain regions likely involved in the pathology of specific disorders. Finally, we suggest that in order to build a more detailed mechanistic understanding of the effects of genetic variants on the brain, future directions in imaging genetics research will require observations of cellular and synaptic structure in specific brain regions beyond the resolution of magnetic resonance imaging. We expect that integrating genetic associations at biological levels from synapse to sulcus will reveal specific causal pathways impacting risk for neuropsychiatric disorders.
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Affiliation(s)
- Brandon D. Le
- Department of Genetics & UNC Neuroscience Center, University of North Carolina at Chapel Hill, USA
| | - Jason L. Stein
- Department of Genetics & UNC Neuroscience Center, University of North Carolina at Chapel Hill, USA
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Yang F, Liu X, Zhao Y, Zhang Y, Wang P, Robinson I, Chen B. Investigation of Three-Dimensional Microstructure of Tricalcium Silicate (C₃S) by Electron Microscopy. MATERIALS 2018; 11:ma11071110. [PMID: 29966230 PMCID: PMC6073500 DOI: 10.3390/ma11071110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/18/2018] [Accepted: 06/27/2018] [Indexed: 11/16/2022]
Abstract
A serial block-face scanning electron microscopy (SBFSEM) system, composed of a scanning electron microscope (SEM) and an ultra-microtome installed within the SEM vacuum chamber, has been used to characterize the three-dimensional (3D) microstructure of tricalcium silicate (C3S) grains embedded in epoxy resin. A selection of C3S grains were segmented and rendered with 3D-image processing software, which allowed the C3S grains to be clearly visualized and enabled statistically quantitative analysis. The results show that about 5% of the C3S grains have volumes larger than 1 μm3 and the average volume of the grains is 25 μm3. Pores can also be clearly seen in the biggest C3S grain, the volume of which is 3.6 × 104 μm3, and the mean volume and total volume of all the pores within this grain are 4.8 μm3 and 3.0 × 103 μm3, respectively. The reported work provides a new approach for the characterization of the 3D spatial structure of raw C3S materials, and the resulting 3D structure of the raw C3S is important for further systematic research on the relationships between the spatial microstructure and the hydration kinetics of C3S and other cement minerals.
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Affiliation(s)
- Fei Yang
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China.
| | - Xianping Liu
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China.
- Key Laboratory of Advanced Civil Engineering Materials (Tongji University), Ministry of Education, Shanghai 201804, China.
| | - Yongjuan Zhao
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China.
| | - Yongming Zhang
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China.
| | - Peiming Wang
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China.
- Key Laboratory of Advanced Civil Engineering Materials (Tongji University), Ministry of Education, Shanghai 201804, China.
| | - Ian Robinson
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China.
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK.
- Division of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, NY 11973, USA.
| | - Bo Chen
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China.
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK.
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Informative three-dimensional survey of cell/tissue architectures in thick paraffin sections by simple low-vacuum scanning electron microscopy. Sci Rep 2018; 8:7479. [PMID: 29748574 PMCID: PMC5945589 DOI: 10.1038/s41598-018-25840-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/30/2018] [Indexed: 01/06/2023] Open
Abstract
Recent advances in bio-medical research, such as the production of regenerative organs from stem cells, require three-dimensional analysis of cell/tissue architectures. High-resolution imaging by electron microscopy is the best way to elucidate complex cell/tissue architectures, but the conventional method requires a skillful and time-consuming preparation. The present study developed a three-dimensional survey method for assessing cell/tissue architectures in 30-µm-thick paraffin sections by taking advantage of backscattered electron imaging in a low-vacuum scanning electron microscope. As a result, in the kidney, the podocytes and their processes were clearly observed to cover the glomerulus. The 30 µm thickness facilitated an investigation on face-side (instead of sectioned) images of the epithelium and endothelium, which are rarely seen within conventional thin sections. In the testis, differentiated spermatozoa were three-dimensionally assembled in the middle of the seminiferous tubule. Further application to vascular-injury thrombus formation revealed the distinctive networks of fibrin fibres and platelets, capturing the erythrocytes into the thrombus. The four-segmented BSE detector provided topographic bird’s-eye images that allowed a three-dimensional understanding of the cell/tissue architectures at the electron-microscopic level. Here, we describe the precise procedures of this imaging method and provide representative electron micrographs of normal rat organs, experimental thrombus formation, and three-dimensionally cultured tumour cells.
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New advances in scanning microscopy and its application to study parasitic protozoa. Exp Parasitol 2018; 190:10-33. [PMID: 29702111 DOI: 10.1016/j.exppara.2018.04.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 04/10/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022]
Abstract
Scanning electron microscopy has been used to observe and study parasitic protozoa for at least 40 years. However, field emission electron sources, as well as improvements in lenses and detectors, brought the resolution power of scanning electron microscopes (SEM) to a new level. Parallel to the refinement of instruments, protocols for preservation of the ultrastructure, immunolabeling, exposure of cytoskeleton and inner structures of parasites and host cells were developed. This review is focused on protozoan parasites of medical and veterinary relevance, e.g., Toxoplasma gondii, Tritrichomonas foetus, Giardia intestinalis, and Trypanosoma cruzi, compilating the main achievements in describing the fine ultrastructure of their surface, cytoskeleton and interaction with host cells. Two new resources, namely, Helium Ion Microscopy (HIM) and Slice and View, using either Focused Ion Beam (FIB) abrasion or Microtome Serial Sectioning (MSS) within the microscope chamber, combined to backscattered electron imaging of fixed (chemically or by quick freezing followed by freeze substitution and resin embedded samples is bringing an exponential amount of valuable information. In HIM there is no need of conductive coating and the depth of field is much higher than in any field emission SEM. As for FIB- and MSS-SEM, high resolution 3-D models of areas and volumes larger than any other technique allows can be obtained. The main results achieved with all these technological tools and some protocols for sample preparation are included in this review. In addition, we included some results obtained with environmental/low vacuum scanning microscopy and cryo-scanning electron microscopy, both promising, but not yet largely employed SEM modalities.
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Stachewicz U, Szewczyk PK, Kruk A, Barber AH, Czyrska-Filemonowicz A. Pore shape and size dependence on cell growth into electrospun fiber scaffolds for tissue engineering: 2D and 3D analyses using SEM and FIB-SEM tomography. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 95:397-408. [PMID: 30573264 DOI: 10.1016/j.msec.2017.08.076] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 07/03/2017] [Accepted: 08/18/2017] [Indexed: 10/19/2022]
Abstract
Electrospun nanofibers have ability to boost cell proliferation in tissue engineered scaffolds as their structure remind cells extra cellular matrix of the native tissue. The complex architecture and network of nanofibrous scaffolds requires advanced characterization methods to understand interrelationship between cells and nanofibers. In our study, we used complementary 2D and 3D analyses of electrospun polylactide-co-glycolide acid (PLGA) scaffolds in two configurations: aligned and randomly oriented nanofibers. Sizes of pores and fibers, pores shapes and porosity, before and after cell culture, were verified by imaging with scanning electron microscopy (SEM) and combination of focus ion beam (FIB) and SEM to obtain 3D reconstructions of samples. Using FIB-SEM tomography for 3D reconstructions and 2D analyses, a unique set of data allowing understanding cell proliferation mechanism into the electrospun scaffolds, was delivered. Critically, the proliferation of cells into nanofibers network depends mainly on the pore shape and pores interconnections, which allow deep integration between cells and nanofibers. The proliferation of cells inside the network of fibers is much limited for aligned fibers comparing to randomly oriented fibers. For random fibers cells have easier way to integrate inside the scaffold as the circularity of pores and their sizes are larger than for aligned scaffolds. The complex architecture of electrospun scaffolds requires appropriate, for tissue engineering needs, cell seeding and culture methods, to maximize tissue growth in vitro environment.
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Affiliation(s)
- Urszula Stachewicz
- AGH University of Science and Technology, International Centre of Electron Microscopy for Materials Science and Faculty of Metals Engineering and Industrial Computer Science, Al. A. Mickiewicza 30, 30-059 Kraków, Poland; School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom.
| | - Piotr K Szewczyk
- AGH University of Science and Technology, International Centre of Electron Microscopy for Materials Science and Faculty of Metals Engineering and Industrial Computer Science, Al. A. Mickiewicza 30, 30-059 Kraków, Poland
| | - Adam Kruk
- AGH University of Science and Technology, International Centre of Electron Microscopy for Materials Science and Faculty of Metals Engineering and Industrial Computer Science, Al. A. Mickiewicza 30, 30-059 Kraków, Poland
| | - Asa H Barber
- School of Engineering, University of Portsmouth, Portsmouth PO1 3DJ, United Kingdom
| | - Aleksandra Czyrska-Filemonowicz
- AGH University of Science and Technology, International Centre of Electron Microscopy for Materials Science and Faculty of Metals Engineering and Industrial Computer Science, Al. A. Mickiewicza 30, 30-059 Kraków, Poland
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The Symbiotic Bacterium Fuels the Energy Metabolism of the Host Trypanosomatid Strigomonas culicis. Protist 2017; 168:253-269. [DOI: 10.1016/j.protis.2017.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 02/02/2017] [Accepted: 02/14/2017] [Indexed: 12/18/2022]
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Claeys M, Yushin VV, Leunissen JL, Claeys J, Bert W. Self-Pressurised Rapid Freezing (SPRF): an easy-to-use and low-cost alternative cryo-fixation method for nematodes. NEMATOLOGY 2017. [DOI: 10.1163/15685411-00003093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Self-Pressurised Rapid Freezing (SPRF), an easy-to-use and low-cost alternative cryo-fixation method, was evaluated based on a comparative analysis of the ultrastructure of spermatozoa of the nematodes Acrobeles complexus and Caenorhabditis elegans. Sealed copper tubes, packed with active nematodes in water, were plunged into nitrogen slush, a semi-solid form of nitrogen. The water inside the capillary copper tube expands upon cooling due to the formation of hexagonal ice, thereby generating high pressure intrinsically for cryo-fixation of the sample. For sperm cells cryo-fixed by SPRF, the preservation of the ultrastructure was comparable to that achieved with high pressure freezing. This was evidenced by the clear details in mitochondria, membranous organelles and cytoskeleton in the pseudopod. It was demonstrated that SPRF fixation did not destroy antigenicity, based on the results of the immunolocalisation of the major sperm protein in both species. In conclusion, SPRF is a low-cost alternative cryo-fixation method for nematodes.
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Affiliation(s)
- Myriam Claeys
- Nematology Research Unit, Department of Biology, Ghent University, Belgium
| | - Vladimir V. Yushin
- National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia
- Far Eastern Federal University, Vladivostok 690950, Russia
| | | | - Jef Claeys
- Nematology Research Unit, Department of Biology, Ghent University, Belgium
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, Belgium
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36
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Karreman MA, Hyenne V, Schwab Y, Goetz JG. Intravital Correlative Microscopy: Imaging Life at the Nanoscale. Trends Cell Biol 2016; 26:848-863. [DOI: 10.1016/j.tcb.2016.07.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 01/04/2023]
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Bisht K, Sharma K, Lacoste B, Tremblay MÈ. Dark microglia: Why are they dark? Commun Integr Biol 2016; 9:e1230575. [PMID: 28042375 PMCID: PMC5193044 DOI: 10.1080/19420889.2016.1230575] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 11/15/2022] Open
Abstract
Using transmission electron microscopy (TEM) we recently characterized a microglial phenotype that is induced by chronic stress, fractalkine receptor deficiency, aging, or Alzheimer disease pathology. These ‘dark’ microglia appear overly active compared with the normal microglia, reaching for synaptic clefts, and extensively engulfing pre-synaptic axon terminals and post-synaptic dendritic spines. From these findings we hypothesized that dark microglia could be specifically implicated in the pathological remodeling of neuronal circuits, which impairs learning, memory, and other essential cognitive functions. In the present addendum we further discuss about the possible causes of their dark appearance under TEM.
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Affiliation(s)
- Kanchan Bisht
- Axe Neurosciences, CRCHU de Québec , Québec City, QC, Canada
| | - Kaushik Sharma
- Axe Neurosciences, CRCHU de Québec , Québec City, QC, Canada
| | - Baptiste Lacoste
- Department of Cellular & Molecular Medicine, Faculty of Medicine, The University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada; Neuroscience Program, The Ottawa Hospital Research Institute, Ottawa, ON, Canada
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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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Augusto I, Monteiro D, Girard-Dias W, Dos Santos TO, Rosa Belmonte SL, Pinto de Oliveira J, Mauad H, da Silva Pacheco M, Lenz D, Stefanon Bittencourt A, Valentim Nogueira B, Lopes Dos Santos JR, Miranda K, Guimarães MCC. Virtual Reconstruction and Three-Dimensional Printing of Blood Cells as a Tool in Cell Biology Education. PLoS One 2016; 11:e0161184. [PMID: 27526196 PMCID: PMC4985121 DOI: 10.1371/journal.pone.0161184] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 08/01/2016] [Indexed: 12/22/2022] Open
Abstract
The cell biology discipline constitutes a highly dynamic field whose concepts take a long time to be incorporated into the educational system, especially in developing countries. Amongst the main obstacles to the introduction of new cell biology concepts to students is their general lack of identification with most teaching methods. The introduction of elaborated figures, movies and animations to textbooks has given a tremendous contribution to the learning process and the search for novel teaching methods has been a central goal in cell biology education. Some specialized tools, however, are usually only available in advanced research centers or in institutions that are traditionally involved with the development of novel teaching/learning processes, and are far from becoming reality in the majority of life sciences schools. When combined with the known declining interest in science among young people, a critical scenario may result. This is especially important in the field of electron microscopy and associated techniques, methods that have greatly contributed to the current knowledge on the structure and function of different cell biology models but are rarely made accessible to most students. In this work, we propose a strategy to increase the engagement of students into the world of cell and structural biology by combining 3D electron microscopy techniques and 3D prototyping technology (3D printing) to generate 3D physical models that accurately and realistically reproduce a close-to-the native structure of the cell and serve as a tool for students and teachers outside the main centers. We introduce three strategies for 3D imaging, modeling and prototyping of cells and propose the establishment of a virtual platform where different digital models can be deposited by EM groups and subsequently downloaded and printed in different schools, universities, research centers and museums, thereby modernizing teaching of cell biology and increasing the accessibility to modern approaches in basic science.
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Affiliation(s)
- Ingrid Augusto
- Laboratório de Ultraestrutura Celular Carlos Alberto Redins, Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Brazil.,Instituto de Biofísica Carlos Chagas Filho e Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Douglas Monteiro
- Instituto de Biofísica Carlos Chagas Filho e Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wendell Girard-Dias
- Instituto de Biofísica Carlos Chagas Filho e Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thaisa Oliveira Dos Santos
- Laboratório de Ultraestrutura Celular Carlos Alberto Redins, Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Brazil
| | | | - Jairo Pinto de Oliveira
- Laboratório de Ultraestrutura Celular Carlos Alberto Redins, Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Helder Mauad
- Departamento de Fisiologia, Universidade Federal do Espírito Santo, Vitória, Brazil
| | | | - Dominik Lenz
- Ciências Farmacêuticas, Universidade de Vila Velha, Vila Velha, Brazil
| | | | - Breno Valentim Nogueira
- Laboratório de Ultraestrutura Celular Carlos Alberto Redins, Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Brazil
| | | | - Kildare Miranda
- Instituto de Biofísica Carlos Chagas Filho e Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marco Cesar Cunegundes Guimarães
- Laboratório de Ultraestrutura Celular Carlos Alberto Redins, Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Brazil
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Kaji T, Kakui K, Miyazaki N, Murata K, Palmer AR. Mesoscale morphology at nanoscale resolution: serial block-face scanning electron microscopy reveals fine 3D detail of a novel silk spinneret system in a tube-building tanaid crustacean. Front Zool 2016; 13:14. [PMID: 27006683 PMCID: PMC4802664 DOI: 10.1186/s12983-016-0146-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/16/2016] [Indexed: 11/22/2022] Open
Abstract
Background The study of morphology is experiencing a renaissance due to rapid improvements in technologies for 3D visualization of complex internal and external structures. But 3D visualization of the internal structure of mesoscale objects — those in the 10–1000 μm range — remains problematic. They are too small for microCT, many lack suitable specific fluorescent markers for confocal microscopy, or they require labor-intensive stacking and smoothing of individual TEM images. Here we illustrate the first comprehensive morphological description of a complete mesoscale biological system at nanoscopic resolution using ultra-modern technology for 3D visualization — serial block-face scanning electron microscopy (SBF-SEM). The SBF-SEM machine combines an in-chamber ultramicrotome, which creates a serial array of exposed surfaces, with an SEM that images each surface as it is exposed. The serial images are then stacked automatically by 3D reconstruction software. We used SBF-SEM to study the spinneret (thread-producing) system of a small, tube-dwelling crustacean that weaves tubes of silk. Thread-producing ability is critical for the survival of many small-bodied animals but the basic morphology of these systems remains mysterious due to the limits of traditional microscopy. Results SBF-SEM allowed us to describe — in full 3D — well-resolved components (glands, ducts, pores, and associated nerves and muscles) of the spinneret system in the thoracic legs and body segments of Sinelobus sp. (Crustacea, Peracarida, Tanaidacea), a tube-building tanaid only 2 mm in body length. The 3D reconstruction by SBF-SEM revealed at nanoscale resolution a unique structure to the gland and duct systems: In each of three thread-producing thoracic segments, two separate ducts, derived from two separate glands located in the body, run through the entire leg and merge at the leg tip just before the spinneret pore opening. We also resolved nerves connecting to individual setae, spines and pores on the walking legs, and individual muscles within each leg segment. Conclusions Our results significantly expand our understanding of the diversity of spinneret systems in the Crustacea by providing the first well-resolved view of spinneret components in the peracarid crustacean order, Tanaidacea. More significantly, our results reveal the great power of SBF-SEM technology for comprehensive studies of the morphology of microscopic animals. Electronic supplementary material The online version of this article (doi:10.1186/s12983-016-0146-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tomonari Kaji
- Systematics and Evolution Group, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9 Canada ; Allgemeine & Spezielle Zoologie, Institut fuer Biowissenschaften, Universität Rostock, Rostock, 18055 Germany
| | - Keiichi Kakui
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Naoyuki Miyazaki
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8585 Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8585 Japan
| | - A Richard Palmer
- Systematics and Evolution Group, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9 Canada
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