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Zheng J, Wu YC, Cai X, Phan P, Er EE, Zhao Z, Lee SSY. Correlative multiscale 3D imaging of mouse primary and metastatic tumors by sequential light sheet and confocal fluorescence microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594162. [PMID: 38798657 PMCID: PMC11118317 DOI: 10.1101/2024.05.14.594162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Three-dimensional (3D) optical microscopy, combined with advanced tissue clearing, permits in situ interrogation of the tumor microenvironment (TME) in large volumetric tumors for preclinical cancer research. Light sheet (also known as ultramicroscopy) and confocal fluorescence microscopy are often used to achieve macroscopic and microscopic 3D images of optically cleared tumor tissues, respectively. Although each technique offers distinct fields of view (FOVs) and spatial resolution, the combination of these two optical microscopy techniques to obtain correlative multiscale 3D images from the same tumor tissues has not yet been explored. To establish correlative multiscale 3D optical microscopy, we developed a method for optically marking defined regions of interest (ROIs) within a cleared mouse tumor by employing a UV light-activated visible dye and Z-axis position-selective UV irradiation in a light sheet microscope system. By integrating this method with subsequent tissue processing, including physical ROI marking, reversal of tissue clearing, tissue macrosectioning, and multiplex immunofluorescence, we established a workflow that enables the tracking and 3D imaging of ROIs within tumor tissues through sequential light sheet and confocal fluorescence microscopy. This approach allowed for quantitative 3D spatial analysis of the immune response in the TME of a mouse mammary tumor following cancer immunotherapy at multiple spatial scales. The workflow also facilitated the direct localization of a metastatic lesion within a whole mouse brain. These results demonstrate that our ROI tracking method and its associated workflow offer a novel approach for correlative multiscale 3D optical microscopy, with the potential to provide new insights into tumor heterogeneity, metastasis, and response to therapy at various spatial levels.
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Neusser TP, Brenzinger B, Schrödl M, Jörger KM. Really a "secondary gill under the skin"? Unveiling "dorsal vessels" in freshwater slugs (Mollusca, Panpulmonata, Acochlidimorpha). J Morphol 2023; 284:e21653. [PMID: 37856274 DOI: 10.1002/jmor.21653] [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: 07/31/2023] [Revised: 09/28/2023] [Accepted: 10/01/2023] [Indexed: 10/21/2023]
Abstract
The freshwater slugs of the genus Acochlidium (Heterobranchia, Gastropoda, and Acochlidimorpha) are peculiar, one to two centimeter sized animals found only in small coastal rivers and streams of Southeast Asian and Western Pacific islands. When first described by Bücking, the author observed a branching "net of dendritic vessels connected to the heart," which he assumed to have replaced the original gastropod gill. In the present study, we compare the renopericardial systems of four Acochlidium species in microanatomical, histological and ultrastructural detail and identify where exactly the enigmatic, subepidermal "dorsal vessels" connect to the renopericardial system to examine if they can really function as a gill. Acochlidium have elaborate renopericardial systems compared to their ancestrally marine and also freshwater relatives. The primary site of ultrafiltration is the epicardium of the atrium with podocytes as usual for gastropods. The "dorsal vessels" in Acochlidium are extensions of the outer epithelium of the pericardial cavity and represent true vessels, that is, coelomatic channels, having an endothelium with podocytes. Hence, they considerably enlarge the site of ultrafiltration increasing the pericardial surface. "Dorsal vessels" in Acochlidium are therefore not homologous to externally similar morphological structures in Sacoglossa (marine panpulmonate slugs and snails). The multiplication of renopericardioducts in Acochlidium is a unique feature within Mollusca that enhances the negative pressure necessary for ultrafiltration in the thin, tube-like dorsal vessels and as a consequence the transport of primary urine from the pericardium to the kidney. The circulatory and excretory systems in Acochlidium are adaptations to a lifestyle in their freshwater environment in which snail bodies are hyposmotic and accrue considerable influx of surplus water into the body, which needs to be expelled.
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Affiliation(s)
| | | | - Michael Schrödl
- LMU Munich, Biocenter, Planegg-Martinsried, Germany
- SNSB, Bavarian State Collection of Zoology, München, Germany
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Marshall AG, Krystofiak E, Damo SM, Hinton A. Correlative light-electron microscopy: integrating dynamics to structure. Trends Biochem Sci 2023; 48:826-827. [PMID: 37277285 DOI: 10.1016/j.tibs.2023.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/20/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Affiliation(s)
- Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Evan Krystofiak
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Steven M Damo
- Department of Life and Physical Sciences, Fisk University, Nashville, TN 37208, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA.
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Jie VW, Miettinen A, Baird E. Novel Methodology for Localizing and Studying Insect Dorsal Rim Area Morphology in 2D and 3D. INSECTS 2023; 14:670. [PMID: 37623380 PMCID: PMC10455470 DOI: 10.3390/insects14080670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Polarized light-based navigation in insects is facilitated by a polarization-sensitive part of the eye, the dorsal rim area (DRA). Existing methods to study the anatomy of the DRA are destructive and time-consuming. We presented a novel method for DRA localization, dissection, and measurement using 3D volumetric images from X-ray micro-computed tomography in combination with 2D photographs. Applying the method on size-polymorphic buff-tailed bumblebees, Bombus terrestris, we found that the DRA was easily obtainable from photographs of the dorsal eye region. Allometric analysis of the DRA in relation to body size in B. terrestris showed that it increased with the body size but not at the same rate. By localizing the DRA of individual bumblebees, we could also perform individual-level descriptions and inter-individual comparisons between the ommatidial structures (lens, crystalline cones, rhabdoms) of three different eye regions (DRA, non-DRA, proximate to DRA). One feature distinct to the bumblebee DRA was the smaller dimension of the crystalline cones in comparison to other regions of the eye. Using our novel methodology, we provide the first individual-level description of DRA ommatidial features and a comparison of how the DRA varies with body size in bumblebees.
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Affiliation(s)
- Vun Wen Jie
- Department of Zoology, Stockholm University, 11418 Stockholm, Sweden;
| | - Arttu Miettinen
- Department of Physics, University of Jyvaskyla, 40014 Jyvaskyla, Finland;
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Emily Baird
- Department of Zoology, Stockholm University, 11418 Stockholm, Sweden;
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Kalke P, Helm C. No cost but high performance-An alternative open source solution for 3D-visualizations in morphology. Microsc Res Tech 2023; 86:193-197. [PMID: 36325733 DOI: 10.1002/jemt.24250] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
Abstract
3D-visualization has become common courtesy in science and also found its way into teaching in schools and universities. Nevertheless, the way to high performance 3D-visualization and analyses remains difficult and is often also a matter of budget. Due to the obvious advantages of presenting morphological and anatomical datasets with the help of 3D-figures, all in one software solutions usually come along with high rental and maintenance fees. For that reason, it is more than overdue to establish and use open source software solutions with all their obvious advantages - as other disciplines already do. Here we provide a modular, highly adaptive and freely available software pipeline for high performance 3D-visualizations of (not only) morphological datasets by combining features of ImageJ, MeshLab and Blender, without any additional costs. Exemplarily using serial-block face SEM data as well as serial AZAN-stained histological sections, the herein presented step-by-step protocol allows for a fast and efficient analysis, visualization and animation of large, anatomical datasets. Regardless which type of serial, morphological datasets needs to be analyzed, our open source guide provides an easy to handle and promptly adaptable solution. Therefore, our pipeline for 3D-visualization represents a valuable alternative to conventional, commercial packages. RESEARCH HIGHLIGHTS: We provide a highly modular and easy to learn open source solution for multiple 3D-visualizations. The step-by-step-guide make it easy to start, and advanced users can replace software, add others and such build your own individual software pipeline.
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Affiliation(s)
- Paul Kalke
- Johann-Friedrich-Blumenbach-Institute for Zoology & Anthropology, Department of Animal Evolution and Biodiversity, Georg-August-University Göttingen, Göttingen, Germany
| | - Conrad Helm
- Johann-Friedrich-Blumenbach-Institute for Zoology & Anthropology, Department of Animal Evolution and Biodiversity, Georg-August-University Göttingen, Göttingen, Germany
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Handschuh S, Glösmann M. Mouse embryo phenotyping using X-ray microCT. Front Cell Dev Biol 2022; 10:949184. [PMID: 36187491 PMCID: PMC9523164 DOI: 10.3389/fcell.2022.949184] [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: 05/20/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Microscopic X-ray computed tomography (microCT) is a structural ex vivo imaging technique providing genuine isotropic 3D images from biological samples at micron resolution. MicroCT imaging is non-destructive and combines well with other modalities such as light and electron microscopy in correlative imaging workflows. Protocols for staining embryos with X-ray dense contrast agents enable the acquisition of high-contrast and high-resolution datasets of whole embryos and specific organ systems. High sample throughput is achieved with dedicated setups. Consequently, microCT has gained enormous importance for both qualitative and quantitative phenotyping of mouse development. We here summarize state-of-the-art protocols of sample preparation and imaging procedures, showcase contemporary applications, and discuss possible pitfalls and sources for artefacts. In addition, we give an outlook on phenotyping workflows using microscopic dual energy CT (microDECT) and tissue-specific contrast agents.
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Kunishima N, Takeda Y, Hirose R, Kume S, Maeda M, Oguchi A, Yanagita M, Shibuya H, Tamura M, Kataoka Y, Murakawa Y, Ito K, Omote K. Compact laboratory-based X-ray microscope enabling nondestructive 3D structure acquisition of mouse nephron with high speed and better user accessibility. Microscopy (Oxf) 2022; 71:315-323. [PMID: 35778966 PMCID: PMC9731380 DOI: 10.1093/jmicro/dfac033] [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: 04/22/2022] [Revised: 06/20/2022] [Accepted: 07/01/2022] [Indexed: 12/15/2022] Open
Abstract
X-ray microscopes adopting computed tomography enable nondestructive 3D visualization of biological specimens at micron-level resolution without conventional 2D serial sectioning that is a destructive/laborious method and is routinely used for analyzing renal biopsy in clinical diagnosis of kidney diseases. Here we applied a compact commercial system of laboratory-based X-ray microscope to observe a resin-embedded osmium-stained 1-mm strip of a mouse kidney piece as a model of renal biopsy, toward a more efficient diagnosis of kidney diseases. A reconstructed computed tomography image from several hours of data collection using CCD detector allowed us to unambiguously segment a single nephron connected to a renal corpuscle, which was consistent with previous reports using serial sectioning. Histogram analysis on the segmented nephron confirmed that the proximal and distal tubules were distinguishable on the basis of their X-ray opacities. A 3D rendering model of the segmented nephron visualized a convoluted structure of renal tubules neighboring the renal corpuscle and a branched structure of efferent arterioles. Furthermore, another data collection using scientific complementary metal-oxide semiconductor detector with a much shorter data acquisition time of 15 min provided similar results from the same samples. These results suggest a potential application of the compact laboratory-based X-ray microscope to analyze mouse renal biopsy.
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Affiliation(s)
| | - Yoshihiro Takeda
- X-ray Research Laboratory, Rigaku Corporation, Akishima, Tokyo 196-8666, Japan
| | - Raita Hirose
- X-ray Research Laboratory, Rigaku Corporation, Akishima, Tokyo 196-8666, Japan
| | - Satoshi Kume
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan,Center for Health Science Innovation, Osaka City University, Osaka 530-0011, Japan
| | - Mitsuyo Maeda
- Multi-Modal Microstructure Analysis Unit, RIKEN-JEOL Collaboration Center, Kobe, Hyogo 650-0047, Japan
| | - Akiko Oguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan,Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Motoko Yanagita
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan,Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Hirotoshi Shibuya
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Yosky Kataoka
- Multi-Modal Microstructure Analysis Unit, RIKEN-JEOL Collaboration Center, Kobe, Hyogo 650-0047, Japan,Laboratory for Cellular Function Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan,Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan,IFOM―the FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Koichiro Ito
- New Market Development Office, Rigaku Corporation, Akishima, Tokyo 196-8666, Japan
| | - Kazuhiko Omote
- X-ray Research Laboratory, Rigaku Corporation, Akishima, Tokyo 196-8666, Japan
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Parlanti P, Cappello V. Microscopes, tools, probes, and protocols: A guide in the route of correlative microscopy for biomedical investigation. Micron 2021; 152:103182. [PMID: 34801960 DOI: 10.1016/j.micron.2021.103182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 12/11/2022]
Abstract
In the last decades, the advancements of microscopes technology, together with the development of new imaging approaches, are trying to address some biological questions that have been unresolved in the past: the need to combine in the same analysis temporal, functional and morphological information on the biological sample has become pressing. For this reason, the use of correlative microscopy, in which two or more imaging techniques are combined in the same analysis, is getting increasingly widespread. In fact, correlative microscopy can overcome limitations of a single imaging method, giving access to a larger amount of information from the same specimen. However, correlative microscopy can be challenging, and appropriate protocols for sample preparation and imaging methods must be selected. Here we review the state of the art of correlating electron microscopy with different imaging methods, focusing on sample preparation, tools, and labeling methods, with the aim to provide a comprehensive guide for those scientists who are approaching the field of correlative methods.
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Affiliation(s)
- Paola Parlanti
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
| | - Valentina Cappello
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
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Paz-Sedano S, Díaz-Agras G, Gosliner TM, Pola M. Revealing morphological characteristics of Goniodorididae genera (Mollusca: Nudibranchia). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00508-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractDetailed knowledge of the anatomy of the species is an essential element in taxonomic studies, since it allows the comparison and differentiation of separate groups of taxa. It becomes especially important when considering type species, as the subsequent identification of the species that compose the taxa is based on its characteristics, considered common in the group. However, despite its relevance, there are still numerous species without detailed descriptions, being especially significant among invertebrates. The family Goniodorididae is a little-known group of nudibranchs that includes eight recognized genera: Okenia, Goniodoris, Ancula, Lophodoris, Spahria, Trapania, Goniodoridella and Murphydoris. Several of their species are not completely described, including type species, and the systematics of the family is still unclear. Here we study in detail the external morphology and internal anatomy of the type species of five of the eight Goniodorididae genera using microcomputed tomography and scanning electron microscopy. We include the species Okenia elegans, Goniodoris nodosa, Ancula gibbosa, Goniodoridella savignyi and Murphydoris singaporensis as well as one species of Trapania, T. graeffei. We describe for the first time the detailed internal anatomy of the type species Goniodoridella savignyi. The diagnostic features of each genus are compared, and a preliminary framework is shown to clarify their systematics and identifications.
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Keklikoglou K, Arvanitidis C, Chatzigeorgiou G, Chatzinikolaou E, Karagiannidis E, Koletsa T, Magoulas A, Makris K, Mavrothalassitis G, Papanagnou ED, Papazoglou AS, Pavloudi C, Trougakos IP, Vasileiadou K, Vogiatzi A. Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques. J Imaging 2021; 7:jimaging7090172. [PMID: 34564098 PMCID: PMC8470083 DOI: 10.3390/jimaging7090172] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 12/12/2022] Open
Abstract
Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digitisation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised.
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Affiliation(s)
- Kleoniki Keklikoglou
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), P.O. Box 2214, 71003 Heraklion, Crete, Greece; (C.A.); (G.C.); (E.C.); (A.M.); (C.P.); (K.V.)
- Biology Department, University of Crete, 70013 Heraklion, Crete, Greece
- Correspondence:
| | - Christos Arvanitidis
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), P.O. Box 2214, 71003 Heraklion, Crete, Greece; (C.A.); (G.C.); (E.C.); (A.M.); (C.P.); (K.V.)
- LifeWatch ERIC, 41071 Seville, Spain
| | - Georgios Chatzigeorgiou
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), P.O. Box 2214, 71003 Heraklion, Crete, Greece; (C.A.); (G.C.); (E.C.); (A.M.); (C.P.); (K.V.)
| | - Eva Chatzinikolaou
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), P.O. Box 2214, 71003 Heraklion, Crete, Greece; (C.A.); (G.C.); (E.C.); (A.M.); (C.P.); (K.V.)
| | - Efstratios Karagiannidis
- First Department of Cardiology, AHEPA University Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (E.K.); (A.S.P.)
| | - Triantafyllia Koletsa
- Department of Pathology, Faculty of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Antonios Magoulas
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), P.O. Box 2214, 71003 Heraklion, Crete, Greece; (C.A.); (G.C.); (E.C.); (A.M.); (C.P.); (K.V.)
| | - Konstantinos Makris
- Medical School, University of Crete, 71003 Heraklion, Crete, Greece; (K.M.); (G.M.); (A.V.)
| | - George Mavrothalassitis
- Medical School, University of Crete, 71003 Heraklion, Crete, Greece; (K.M.); (G.M.); (A.V.)
- IMBB, FORTH, 70013 Heraklion, Crete, Greece
| | - Eleni-Dimitra Papanagnou
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece; (E.-D.P.); (I.P.T.)
| | - Andreas S. Papazoglou
- First Department of Cardiology, AHEPA University Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (E.K.); (A.S.P.)
| | - Christina Pavloudi
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), P.O. Box 2214, 71003 Heraklion, Crete, Greece; (C.A.); (G.C.); (E.C.); (A.M.); (C.P.); (K.V.)
| | - Ioannis P. Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece; (E.-D.P.); (I.P.T.)
| | - Katerina Vasileiadou
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), P.O. Box 2214, 71003 Heraklion, Crete, Greece; (C.A.); (G.C.); (E.C.); (A.M.); (C.P.); (K.V.)
| | - Angeliki Vogiatzi
- Medical School, University of Crete, 71003 Heraklion, Crete, Greece; (K.M.); (G.M.); (A.V.)
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Franke M, Geier B, Hammel JU, Dubilier N, Leisch N. Coming together-symbiont acquisition and early development in deep-sea bathymodioline mussels. Proc Biol Sci 2021; 288:20211044. [PMID: 34403628 PMCID: PMC8370805 DOI: 10.1098/rspb.2021.1044] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
How and when symbionts are acquired by their animal hosts has a profound impact on the ecology and evolution of the symbiosis. Understanding symbiont acquisition is particularly challenging in deep-sea organisms because early life stages are so rarely found. Here, we collected early developmental stages of three deep-sea bathymodioline species from different habitats to identify when these acquire their symbionts and how their body plan adapts to a symbiotic lifestyle. These mussels gain their nutrition from chemosynthetic bacteria, allowing them to thrive at deep-sea vents and seeps worldwide. Correlative imaging analyses using synchrotron-radiation based microtomography together with light, fluorescence and electron microscopy revealed that the pediveliger larvae were aposymbiotic. Symbiont colonization began during metamorphosis from a planktonic to a benthic lifestyle, with the symbionts rapidly colonizing first the gills, the symbiotic organ of adults, followed by all other epithelia of their hosts. Once symbiont densities in plantigrades reached those of adults, the host's intestine changed from the looped anatomy typical for bivalves to a straightened form. Within the Mytilidae, this morphological change appears to be specific to Bathymodiolus and Gigantidas, and is probably linked to the decrease in the importance of filter feeding when these mussels switch to gaining their nutrition largely from their symbionts.
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Affiliation(s)
- Maximilian Franke
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
- MARUM—Zentrum für Marine Umweltwissenschaften, University of Bremen, Leobener Strasse 2, 28359 Bremen, Germany
| | - Benedikt Geier
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
| | - Jörg U. Hammel
- Helmholtz-Zentrum Hereon, Institute of Materials Physics, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
- MARUM—Zentrum für Marine Umweltwissenschaften, University of Bremen, Leobener Strasse 2, 28359 Bremen, Germany
| | - Nikolaus Leisch
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
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MicroCT as a Useful Tool for Analysing the 3D Structure of Lichens and Quantifying Internal Cephalodia in Lobaria pulmonaria. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1020015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
High-resolution X-ray computer tomography (microCT) is a well-established technique to analyse three-dimensional microstructures in 3D non-destructive imaging. The non-destructive three-dimensional analysis of lichens is interesting for many reasons. The examination of hidden structural characteristics can, e.g., provide information on internal structural features (form and distribution of fungal-supporting tissue/hypha), gas-filled spaces within the thallus (important for gas exchange and, thus, physiological processes), or yield information on the symbiont composition within the lichen, e.g., the localisation and amount of additional cyanobacteria in cephalodia. Here, we present the possibilities and current limitations for applying conventional laboratory-based high-resolution X-ray computer tomography to analyse lichens. MicroCT allows the virtual 3D reconstruction of a sample from 2D X-ray projections and is helpful for the non-destructive analysis of structural characters or the symbiont composition of lichens. By means of a quantitative 3D image analysis, the volume of internal cephalodia is determined for Lobaria pulmonaria and the external cephalodia of Peltigera leucophlebia. Nevertheless, the need for higher-resolution tomography for more detailed studies is emphasised. Particular challenges are the large sizes of datasets to be analysed and the high variability of the lichen microstructures.
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Connecting structure and function from organisms to molecules in small-animal symbioses through chemo-histo-tomography. Proc Natl Acad Sci U S A 2021; 118:2023773118. [PMID: 34183413 PMCID: PMC8300811 DOI: 10.1073/pnas.2023773118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Metabolites mediate the establishment and persistence of most interkingdom symbioses. Still, to pinpoint the metabolites each partner displays upon interaction remains the biggest challenge in studying multiorganismal assemblages. Addressing this challenge, we developed a correlative imaging workflow to connect the in situ production of metabolites with the organ-scale and cellular three-dimensional distributions of mutualistic and pathogenic (micro)organisms in the same host animal. Combining mass spectrometry imaging and micro-computed X-ray tomography provided a culture-independent approach, which is essential to include the full spectrum of naturally occurring interactions. To introduce the potential of combining high-resolution tomography with metabolite imaging, we resolved the metabolic interactions between an invertebrate host, its symbiotic bacteria, and tissue parasites at unprecedented detail for model and nonmodel symbioses. Our understanding of metabolic interactions between small symbiotic animals and bacteria or parasitic eukaryotes that reside within their bodies is extremely limited. This gap in knowledge originates from a methodological challenge, namely to connect histological changes in host tissues induced by beneficial and parasitic (micro)organisms to the underlying metabolites. We addressed this challenge and developed chemo-histo-tomography (CHEMHIST), a culture-independent approach to connect anatomic structure and metabolic function in millimeter-sized symbiotic animals. CHEMHIST combines chemical imaging of metabolites based on mass spectrometry imaging (MSI) and microanatomy-based micro-computed X-ray tomography (micro-CT) on the same animal. Both high-resolution MSI and micro-CT allowed us to correlate the distribution of metabolites to the same animal’s three-dimensional (3D) histology down to submicrometer resolutions. Our protocol is compatible with tissue-specific DNA sequencing and fluorescence in situ hybridization for the taxonomic identification and localization of the associated micro(organisms). Building CHEMHIST upon in situ imaging, we sampled an earthworm from its natural habitat and created an interactive 3D model of its physical and chemical interactions with bacteria and parasitic nematodes in its tissues. Combining MSI and micro-CT, we present a methodological groundwork for connecting metabolic and anatomic phenotypes of small symbiotic animals that often represent keystone species for ecosystem functioning.
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Rother L, Kraft N, Smith DB, El Jundi B, Gill RJ, Pfeiffer K. A micro-CT-based standard brain atlas of the bumblebee. Cell Tissue Res 2021; 386:29-45. [PMID: 34181089 PMCID: PMC8526489 DOI: 10.1007/s00441-021-03482-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/03/2021] [Indexed: 02/07/2023]
Abstract
In recent years, bumblebees have become a prominent insect model organism for a variety of biological disciplines, particularly to investigate learning behaviors as well as visual performance. Understanding these behaviors and their underlying neurobiological principles requires a clear understanding of brain anatomy. Furthermore, to be able to compare neuronal branching patterns across individuals, a common framework is required, which has led to the development of 3D standard brain atlases in most of the neurobiological insect model species. Yet, no bumblebee 3D standard brain atlas has been generated. Here we present a brain atlas for the buff-tailed bumblebee Bombus terrestris using micro-computed tomography (micro-CT) scans as a source for the raw data sets, rather than traditional confocal microscopy, to produce the first ever micro-CT-based insect brain atlas. We illustrate the advantages of the micro-CT technique, namely, identical native resolution in the three cardinal planes and 3D structure being better preserved. Our Bombus terrestris brain atlas consists of 30 neuropils reconstructed from ten individual worker bees, with micro-CT allowing us to segment neuropils completely intact, including the lamina, which is a tissue structure often damaged when dissecting for immunolabeling. Our brain atlas can serve as a platform to facilitate future neuroscience studies in bumblebees and illustrates the advantages of micro-CT for specific applications in insect neuroanatomy.
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Affiliation(s)
- Lisa Rother
- Department of Behavioral Physiology and Sociobiology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Nadine Kraft
- Department of Behavioral Physiology and Sociobiology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Dylan B Smith
- Department of Life Sciences, Imperial College London, Silwood Park, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Basil El Jundi
- Department of Behavioral Physiology and Sociobiology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Richard J Gill
- Department of Life Sciences, Imperial College London, Silwood Park, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Keram Pfeiffer
- Department of Behavioral Physiology and Sociobiology, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
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Reproductive biology, embryonic development and matrotrophy in the phylactolaemate bryozoan Plumatella casmiana. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00497-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractBryozoa is a phylum of aquatic, colonial suspension-feeders within the Lophotrochozoa. In the Phylactolaemata embryonic development occurs in an internal brood sac on the body wall accompanied by extraembryonic nutrition. Owing to previous contradictive descriptions, many aspects of their sexual reproduction require restudy. Consequently, this study analyses embryogenesis of the freshwater bryozoan Plumatella casmiana by serial sections, 3D reconstruction and transmission electron microscopy. Early embryos cleave and soon develop into blastulae with a small central cavity. The mesoderm forms by delamination starting from the distal side towards the proximal end. In later embryos two polypides form on the posterior side that ultimately will be covered by a ciliated mantle in the larva. Embryos increase in size during development and form temporary cell contacts to the embryo sac. Mesodermal cells of the embryo sac show signs of transcellular transport indicating that embryos are nourished by transferring nutrients from the maternal coelom towards the brood cavity. This study clarifies several details such as mesoderm formation and the onset of bud development. Embryos are connected to their respective embryo sacs by a variety of temporary cytoplasmic processes formed by both tissues during embryogenesis, including a ‘placental’ ring zone. Although ultrastructural data of these cell contacts are not entirely conclusive about their function, we suggest that embryos absorb nutrients via the entire surface. The close opposition of embryos to the embryo sac implies placentation as matrotrophic mode in phylactolaemate bryozoans, with embryo sacs acting as placental analogues.
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Holst S, Miranda LS, Meyer P, Michalik P, Sötje I. Morphological analyses of the adult and juvenile stages of the stalked jellyfish Craterolophus convolvulus (Johnston, 1835) (Cnidaria: Staurozoa: Stauromedusae: Craterolophidae) using micro-CT. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Multiscale ATUM-FIB Microscopy Enables Targeted Ultrastructural Analysis at Isotropic Resolution. iScience 2020; 23:101290. [PMID: 32622266 PMCID: PMC7334410 DOI: 10.1016/j.isci.2020.101290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/11/2020] [Accepted: 06/15/2020] [Indexed: 12/24/2022] Open
Abstract
Volume electron microscopy enables the ultrastructural analysis of biological tissue. Currently, the techniques involving ultramicrotomy (ATUM, ssTEM) allow large fields of view but afford only limited z-resolution, whereas ion beam-milling approaches (FIB-SEM) yield isotropic voxels but are restricted in volume size. Now we present a hybrid method, named ATUM-FIB, which combines the advantages of both approaches. ATUM-FIB is based on serial sectioning of tissue into “semithick” (2–10 μm) sections collected onto tape. Serial light and electron microscopy allows the identification of regions of interest that are then directly accessible for targeted FIB-SEM. The set of semithick sections thus represents a tissue “library” which provides three-dimensional context information that can be probed “on demand” by local high-resolution analysis. We demonstrate the potential of this technique to reveal the ultrastructure of rare but pathologically important events by identifying microglia contact sites with amyloid plaques in a mouse model of familial Alzheimer's disease. Fast nanometer-resolution relocation and 3D imaging of preselected structures Transparent tape-based multiscale light and volume electron microscopy Heated ultramicrotomy at 2–10 μm with precured epoxy resin
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19
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Ferstl S, Schwaha T, Ruthensteiner B, Hehn L, Allner S, Müller M, Dierolf M, Achterhold K, Pfeiffer F. Nanoscopic X-ray tomography for correlative microscopy of a small meiofaunal sea-cucumber. Sci Rep 2020; 10:3960. [PMID: 32127610 PMCID: PMC7054411 DOI: 10.1038/s41598-020-60977-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/19/2020] [Indexed: 01/18/2023] Open
Abstract
In the field of correlative microscopy, light and electron microscopy form a powerful combination for morphological analyses in zoology. Due to sample thickness limitations, these imaging techniques often require sectioning to investigate small animals and thereby suffer from various artefacts. A recently introduced nanoscopic X-ray computed tomography (NanoCT) setup has been used to image several biological objects, none that were, however, embedded into resin, which is prerequisite for a multitude of correlative applications. In this study, we assess the value of this NanoCT for correlative microscopy. For this purpose, we imaged a resin-embedded, meiofaunal sea cucumber with an approximate length of 1 mm, where microCT would yield only little information about the internal anatomy. The resulting NanoCT data exhibits isotropic 3D resolution, offers deeper insights into the 3D microstructure, and thereby allows for a complete morphological characterization. For comparative purposes, the specimen was sectioned subsequently to evaluate the NanoCT data versus serial sectioning light microscopy (ss-LM). To correct for mechanical instabilities and drift artefacts, we applied an alternative alignment procedure for CT reconstruction. We thereby achieve a level of detail on the subcellular scale comparable to ss-LM images in the sectioning plane.
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Affiliation(s)
- Simone Ferstl
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748, Garching, Germany.
| | - Thomas Schwaha
- Department of Integrative Zoology, University of Vienna, 1090, Vienna, Austria
| | | | - Lorenz Hehn
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748, Garching, Germany
| | - Sebastian Allner
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748, Garching, Germany
| | - Mark Müller
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748, Garching, Germany
| | - Martin Dierolf
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748, Garching, Germany
| | - Klaus Achterhold
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748, Garching, Germany
| | - Franz Pfeiffer
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748, Garching, Germany
- Department of Diagnostic and Interventional Radiology, School of Medicine and Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
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20
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Abstract
Micro-computed X-ray tomography (μCT) coupled with visualization techniques such as three-dimensional reconstruction of internal morphological structures has opened up new pathways for analyzing the anatomy of nervous systems in intact specimens. The possibility for combining μCT with other techniques is one of the major advantages of μCT scanning, and the technical development of higher resolutions in lab-based μCT-scanners allows for investigating the anatomy of specimens in the sub-milimeter range. The European shore crab Carcinus maenas features a larval development over four zoeal and one megalopal stage with body lengths ranging from 500 μm to 2000 μm. The developing nervous system in the larvae of C. maenas is organized into a central brain which is connected via esophageal connectives with a ventral nerve chord and segmental ganglia. Since soft tissues such as the nervous tissues feature low contrasts compared to other tissues such as muscles or cuticularized body parts, the interpretation in μCT scans is challenging and needs some practice. The protocol described here is also applicable for larger specimens of a variety of species and spans over 2-3 days resulting in an image stack ready for postprocessing and visualization.
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Affiliation(s)
- Jakob Krieger
- Department of Cytology and Evolutionary Biology, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany.
| | - Franziska Spitzner
- Department of Cytology and Evolutionary Biology, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
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21
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Dederichs TM, Müller CHG, Sentenská L, Lipke E, Uhl G, Michalik P. The innervation of the male copulatory organ of spiders (Araneae) - a comparative analysis. Front Zool 2019; 16:39. [PMID: 31666802 PMCID: PMC6813115 DOI: 10.1186/s12983-019-0337-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/05/2019] [Indexed: 01/23/2023] Open
Abstract
Background Nervous tissue is an inherent component of the many specialized genital structures for transferring sperm directly into the female’s body. However, the male copulatory organ of spiders was considered a puzzling exception. Based on the recent discovery of nervous tissue in the pedipalps of two distantly related spider species, we investigated representatives of all major groups across the spider tree of life for the presence of palpal nerves. We used a correlative approach that combined histology, micro-computed tomography and electron microscopy. Results We show that the copulatory organ is innervated in all species investigated. There is a sensory organ at the base of the sperm transferring sclerite in several taxa and nervous tissue occurs close to the glandular tissue of the spermophor, where sperm are stored before transfer. Conclusions The innervation of the copulatory organ by the bulb nerve and associated efferent fibers is part of the ground pattern of spiders. Our findings pave the way for unraveling the sensory interaction of genitalia during mating and for the still enigmatic mode of uptake and release of sperm from the male copulatory organ.
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Affiliation(s)
- Tim M Dederichs
- 1Department of General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Loitzer Straße 26, 17489 Greifswald, Germany
| | - Carsten H G Müller
- 1Department of General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Loitzer Straße 26, 17489 Greifswald, Germany
| | - Lenka Sentenská
- 2Department of Botany and Zoology, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Elisabeth Lipke
- German Air Force Center of Aerospace Medicine, Straße der Luftwaffe 322, 82256 Fürstenfeldbruck, Germany
| | - Gabriele Uhl
- 1Department of General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Loitzer Straße 26, 17489 Greifswald, Germany
| | - Peter Michalik
- 1Department of General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Loitzer Straße 26, 17489 Greifswald, Germany
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22
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Burnett TL, Withers PJ. Completing the picture through correlative characterization. NATURE MATERIALS 2019; 18:1041-1049. [PMID: 31209389 DOI: 10.1038/s41563-019-0402-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 05/15/2019] [Indexed: 05/28/2023]
Abstract
Natural and manufactured materials rely on complex hierarchical microstructures to deliver a suite of interesting properties. To predict and tailor their performance requires a joined-up knowledge of their multiphase microstructure, interfaces, chemistry and crystallography from the nanoscale to the macroscale. This Perspective reflects on how recent developments in correlative characterization can bring together multiple image modalities and maps of the local chemistry, structure and functionality to form rich multimodal and multiscale correlated datasets. The automated collection and digitization of multidimensional data is an essential part of the picture for developing multiscale modelling and 'big data'-driven machine learning approaches. These are needed to both improve our understanding of existing materials and exploit high-throughput combinatorial synthesis, processing and testing methods to develop materials with bespoke properties.
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Affiliation(s)
- T L Burnett
- Henry Royce Institute for Advanced Materials, School of Materials, The University of Manchester, Manchester, UK
| | - P J Withers
- Henry Royce Institute for Advanced Materials, School of Materials, The University of Manchester, Manchester, UK.
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23
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Mitchell RL, Coleman M, Davies P, North L, Pope EC, Pleydell-Pearce C, Harris W, Johnston R. Macro-to-nanoscale investigation of wall-plate joints in the acorn barnacle Semibalanus balanoides: correlative imaging, biological form and function, and bioinspiration. J R Soc Interface 2019; 16:20190218. [PMID: 31387487 PMCID: PMC6731510 DOI: 10.1098/rsif.2019.0218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/25/2019] [Indexed: 11/12/2022] Open
Abstract
Correlative imaging combines information from multiple modalities (physical-chemical-mechanical properties) at various length scales (centimetre to nanometre) to understand the complex biological materials across dimensions (2D-3D). Here, we have used numerous coupled systems: X-ray microscopy (XRM), scanning electron microscopy (SEM), electron backscatter diffraction (EBSD), optical light microscopy (LM) and focused ion beam (FIB-SEM) microscopy to ascertain the microstructural and crystallographic properties of the wall-plate joints in the barnacle Semibalanus balanoides. The exoskeleton is composed of six interlocking wall plates, and the interlocks between neighbouring plates (alae) allow barnacles to expand and grow while remaining sealed and structurally strong. Our results indicate that the ala contain functionally graded orientations and microstructures in their crystallography, which has implications for naturally functioning microstructures, potential natural strengthening and preferred oriented biomineralization. Elongated grains at the outer edge of the ala are oriented perpendicularly to the contact surface, and the c-axis rotates with the radius of the ala. Additionally, we identify for the first time three-dimensional nanoscale ala pore networks revealing that the pores are only visible at the tip of the ala and that pore thickening occurs on the inside (soft bodied) edge of the plates. The pore networks appear to have the same orientation as the oriented crystallography, and we deduce that the pore networks are probably organic channels and pockets, which are involved with the biomineralization process. Understanding these multiscale features contributes towards an understanding of the structural architecture in barnacles, but also their consideration for bioinspiration of human-made materials. The work demonstrates that correlative methods spanning different length scales, dimensions and modes enable the extension of the structure-property relationships in materials to form and function of organisms.
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Affiliation(s)
- R. L. Mitchell
- Advanced Imaging of Materials (AIM) Facility, College of Engineering, Swansea University, Swansea SA1 8EN, UK
| | - M. Coleman
- Advanced Imaging of Materials (AIM) Facility, College of Engineering, Swansea University, Swansea SA1 8EN, UK
| | - P. Davies
- Advanced Imaging of Materials (AIM) Facility, College of Engineering, Swansea University, Swansea SA1 8EN, UK
| | - L. North
- Advanced Imaging of Materials (AIM) Facility, College of Engineering, Swansea University, Swansea SA1 8EN, UK
| | - E. C. Pope
- Department of Biosciences, Swansea University, Swansea SA2 8PP, UK
| | - C. Pleydell-Pearce
- Advanced Imaging of Materials (AIM) Facility, College of Engineering, Swansea University, Swansea SA1 8EN, UK
| | - W. Harris
- Carl Zeiss Microscopy, Pleasanton, CA 94588, USA
| | - R. Johnston
- Advanced Imaging of Materials (AIM) Facility, College of Engineering, Swansea University, Swansea SA1 8EN, UK
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Jacob DE, Ruthensteiner B, Trimby P, Henry H, Martha SO, Leitner J, Otter LM, Scholz J. Architecture of Anoteropora latirostris (Bryozoa, Cheilostomata) and implications for their biomineralization. Sci Rep 2019; 9:11439. [PMID: 31391508 PMCID: PMC6685955 DOI: 10.1038/s41598-019-47848-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/24/2019] [Indexed: 11/09/2022] Open
Abstract
Cheilostome Bryozoa Anoteropora latirostris, a colonial marine invertebrate, constructs its skeleton from calcite and aragonite. This study presents firstly correlated multi-scale electron microscopy, micro-computed tomography, electron backscatter diffraction and NanoSIMS mapping. We show that all primary, coarse-grained platy calcitic lateral walls are covered by fine-grained fibrous aragonite. Vertical lateral walls separating autozooid chambers have aragonite only on their distal side. This type of asymmetric mineralization of lateral walls results from the vertical arrangement of the zooids at the growth margins of the colony and represents a type of biomineralization previously unknown in cheilostome bryozoans. NanoSIMS mapping across the aragonite-calcite interface indicates an organic layer between both mineral phases, likely representing an organic template for biomineralization of aragonite on the calcite layer. Analysis of crystallographic orientations show a moderately strong crystallographic preferred orientation (CPO) for calcite (7.4 times random orientation) and an overall weaker CPO for aragonite (2.4 times random orientation) with a high degree of twinning (45%) of the aragonite grains. The calculated Young's modulus for the CPO map shows a weak mechanical direction perpendicular to the colony's upper surface facilitating this organism's strategy of clonal reproduction by fragmentation along the vertical zooid walls.
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Affiliation(s)
- D E Jacob
- Department of Earth and Planetary Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
| | - B Ruthensteiner
- Zoologische Staatssammlung München, Staatliche Naturwissenschaftliche Sammlung Bayerns, Münchhausenstraße 21, 81247, München, Germany
| | - P Trimby
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Oxford Instruments Nanoanalysis, High Wycombe, UK
| | - H Henry
- Department of Earth and Planetary Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
- Australian Research Council Centre of Excellence for Core to Crust Fluid System (CCFS)/GEMOC, Macquarie University, North Ryde, Australia
| | - S O Martha
- Senckenberg Forschungsinstitute und Naturmuseen, Marine Evertebraten III, Senckenberganlage 25, Frankfurt, Germany
| | - J Leitner
- Max Planck Institute for Chemistry, Particle Chemistry, Hahn-Meitner-Weg 1, Mainz, Germany
| | - L M Otter
- Department of Earth and Planetary Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - J Scholz
- Senckenberg Forschungsinstitute und Naturmuseen, Marine Evertebraten III, Senckenberganlage 25, Frankfurt, Germany
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25
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Parapar J, Caramelo C, Candás M, Cunha-Veira X, Moreira J. An integrative approach to the anatomy of Syllis gracilis Grube, 1840 (Annelida) using micro-computed X-ray tomography. PeerJ 2019; 7:e7251. [PMID: 31328035 PMCID: PMC6622173 DOI: 10.7717/peerj.7251] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/13/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The overall anatomy of the genus Syllis (Annelida: Syllidae) has been largely studied; however, an integrative approach considering different anatomical techniques has never been considered. Here, we use micro-computed X-ray tomography (micro-CT) to examine the internal anatomy of Syllis gracilis Grube, 1840, along with other widely available techniques. METHODS We studied the anatomy of the marine annelid S. gracilis through an integrative approach, including micro-CT along with stereo and light compound microscopy (STM, LCM), scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM) and histological sectioning (HIS). In this manner, we evaluated the applicability of micro-CT for the examination of annelid anatomy by testing whether the images obtained make it possible to visualize the main body structures, in comparison with other current techniques, of the various elements of its internal anatomy. RESULTS Overall external and internal body elements are clearly shown by the integrative use of all techniques, thus overcoming the limitations of each when studied separately.Any given method shows disparate results, depending on the body part considered. For instance, micro-CT provided good images of the external anatomy, including relevant characters such as the shape, length and number of articles of dorsal parapodial cirri. However, it is especially useful for the examination of internal anatomy, thus allowing for 3D visualization of the natural spatial arrangement of the different organs. The features best visualized are those of higher tissue density (i.e., body musculature, anterior parts of the digestive tract), particularly in 3D images of unstained specimens, whereas less electrodense tissues (i.e., the peritoneal lining of septa and nervous system) are less clearly visualized. The use of iodine stain with micro-CT has shown advantages against non-staining for the adequate observation of delicate elements of low density, such as the segmental organs, the connective between the ganglia, the ventral nerve cord and segmental nerves. DISCUSSION Main external anatomical elements of S. gracilis are well shown with micro-CT, but images show lesser optical resolution and contrast when compared to micrographs provided by SEM and CLSM, especially for fine structural features of chaetae. Comparison of micro-CT and HIS images revealed the utility and reliability of the former to show the presence, shape and spatial disposition of most internal body organs; the resolution of micro-CT images at a cellular level is, however, much lower than that of HIS, which makes both techniques complementary.
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Affiliation(s)
- Julio Parapar
- Departamento de Bioloxía, Universidade da Coruña, A Coruña, Spain
| | - Carlos Caramelo
- Departamento de Bioloxía, Universidade da Coruña, A Coruña, Spain
| | - María Candás
- Estación de Bioloxía Mariña da Graña, Universidade de Santiago de Compostela, Ferrol, Spain
| | - Xela Cunha-Veira
- Estación de Bioloxía Mariña da Graña, Universidade de Santiago de Compostela, Ferrol, Spain
| | - Juan Moreira
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
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26
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Johnson Chacko L, Wertjanz D, Sergi C, Dudas J, Fischer N, Eberharter T, Hoermann R, Glueckert R, Fritsch H, Rask-Andersen H, Schrott-Fischer A, Handschuh S. Growth and cellular patterning during fetal human inner ear development studied by a correlative imaging approach. BMC DEVELOPMENTAL BIOLOGY 2019; 19:11. [PMID: 31109306 PMCID: PMC6528216 DOI: 10.1186/s12861-019-0191-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/12/2019] [Indexed: 02/04/2023]
Abstract
Background Progressive transformation of the otic placode into the functional inner ear during gestational development in humans leads to the acquisition of hearing perception via the cochlea and balance and spatial orientation via the vestibular organ. Results Using a correlative approach involving micro-computerized tomography (micro-CT), transmission electron microscopy and histological techniques we were able to examine both the morphological and cellular changes associated with human inner ear development. Such an evaluation allowed for the examination of 3D geometry with high spatial and temporal resolution. In concert with gestational progression and growth of the cochlear duct, an increase in the distance between some of the Crista ampullaris is evident in all the specimens examined from GW12 to GW36. A parallel increase in the distances between the macular organs - fetal utricle and saccule - is also evident across the gestational stages examined. The distances between both the utricle and saccule to the three cristae ampullares also increased across the stages examined. A gradient in hair cell differentiation is apparent from apex to base of the fetal cochlea even at GW14. Conclusion We present structural information on human inner ear development across multiple levels of biological organization, including gross-morphology of the inner ear, cellular and subcellular details of hearing and vestibular organs, as well as ultrastructural details in the developing sensory epithelia. This enabled the gathering of detailed information regarding morphometric changes as well in realizing the complex developmental patterns of the human inner ear. We were able to quantify the volumetric and linear aspects of selected gestational inner ear specimens enabling a better understanding of the cellular changes across the fetal gestational timeline. Moreover, these data could serve as a reference for better understanding disorders that arise during inner ear development. Electronic supplementary material The online version of this article (10.1186/s12861-019-0191-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lejo Johnson Chacko
- Department of Otorhinolaryngology, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - David Wertjanz
- Department of Otorhinolaryngology, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Consolato Sergi
- Department of Laboratory Medicine & Pathology, Division of Anatomical Pathology, 5B4.09 Walter C MacKenzie Health Sciences Centre, University of Alberta, Alberta, Canada
| | - Jozsef Dudas
- Department of Otorhinolaryngology, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Natalie Fischer
- Department of Otorhinolaryngology, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Theresa Eberharter
- Department of Otorhinolaryngology, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Romed Hoermann
- Department of Anatomy, Histology & Embryology, Division of Clinical & Functional Anatomy, Medical University of Innsbruck, Muellerstrasse 59, 6020, Innsbruck, Austria
| | - Rudolf Glueckert
- Department of Otorhinolaryngology, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria.,University Clinics Innsbruck, Tirol Kliniken, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Helga Fritsch
- Department of Anatomy, Histology & Embryology, Division of Clinical & Functional Anatomy, Medical University of Innsbruck, Muellerstrasse 59, 6020, Innsbruck, Austria
| | - Helge Rask-Andersen
- Department of Surgical Sciences, Head and Neck Surgery, Section of Otolaryngology, Uppsala University Hospital, 751 85, Uppsala, SE, Sweden
| | - Anneliese Schrott-Fischer
- Department of Otorhinolaryngology, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria.
| | - Stephan Handschuh
- VetCore Facility for Research, Imaging Unit, University of Veterinary Medicine Vienna, Veterinaerplatz 1, A-1210, Vienna, Austria
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27
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Albers J, Pacilé S, Markus MA, Wiart M, Vande Velde G, Tromba G, Dullin C. X-ray-Based 3D Virtual Histology-Adding the Next Dimension to Histological Analysis. Mol Imaging Biol 2019; 20:732-741. [PMID: 29968183 DOI: 10.1007/s11307-018-1246-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Histology and immunohistochemistry of thin tissue sections have been the standard diagnostic procedure in many diseases for decades. This method is highly specific for particular tissue regions or cells, but mechanical sectioning of the specimens is required, which destroys the sample in the process and can lead to non-uniform tissue deformations. In addition, regions of interest cannot be located beforehand and the analysis is intrinsically two-dimensional. Micro X-ray computed tomography (μCT) on the other hand can provide 3D images at high resolution and allows for quantification of tissue structures, as well as the localization of small regions of interest. These advantages advocate the use of μCT for virtual histology tool with or without subsequent classical histology. This review summarizes the most recent examples of virtual histology and provides currently known possibilities of improving contrast and resolution of μCT. Following a background in μCT imaging, ex vivo staining procedures for contrast enhancement are presented as well as label-free virtual histology approaches and the technologies, which could rapidly advance it, such as phase-contrast CT. Novel approaches such as zoom tomography and nanoparticulate contrast agents will also be considered. The current evidence suggests that virtual histology may present a valuable addition to the workflow of histological analysis, potentially reducing the workload in pathology, refining tissue classification, and supporting the detection of small malignancies.
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Affiliation(s)
- J Albers
- Institute for Diagnostic and Interventional Radiology, University Medical Center Göttingen, Göttingen, Germany
| | - S Pacilé
- Department of Engineering and Architecture, University of Trieste, Trieste, Italy.,Elettra Sincrotrone Trieste, Trieste, Italy
| | - M A Markus
- Translational Molecular Imaging, Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - M Wiart
- Univ Lyon, CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, 69500, Bron, France
| | - G Vande Velde
- Department of Imaging and Pathology, Faculty of Medicine, KU Leuven-University of Leuven, Leuven, Belgium
| | - G Tromba
- Elettra Sincrotrone Trieste, Trieste, Italy
| | - C Dullin
- Institute for Diagnostic and Interventional Radiology, University Medical Center Göttingen, Göttingen, Germany. .,Elettra Sincrotrone Trieste, Trieste, Italy. .,Translational Molecular Imaging, Max-Planck-Institute for Experimental Medicine, Göttingen, Germany.
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28
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Schlüter S, Eickhorst T, Mueller CW. Correlative Imaging Reveals Holistic View of Soil Microenvironments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:829-837. [PMID: 30525511 DOI: 10.1021/acs.est.8b05245] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The microenvironmental conditions in soil exert a major control on many ecosystem functions of soil. Their investigation in intact soil samples is impaired by methodological challenges in the joint investigation of structural heterogeneity that defines pathways for matter fluxes and biogeochemical heterogeneity that governs reaction patterns and microhabitats. Here we demonstrate how these challenges can be overcome with a novel protocol for correlative imaging based on image registration to combine three-dimensional microstructure analysis of X-ray tomography data with biogeochemical microscopic data of various modalities and scales (light microscopy, fluorescence microscopy, electron microscopy, secondary ion mass spectrometry). Correlative imaging of a microcosm study shows that the majority (75%) of bacteria are located in mesopores (<10 μm). Furthermore, they have a preference to forage near macropore surfaces and near fresh particulate organic matter. Ignoring the structural complexity coming from the third dimension is justified for metrics based on size and distances but leads to a substantial bias for metrics based on continuity. This versatile combination of imaging modalities with freely available software and protocols may open up completely new avenues for the investigation of many important biogeochemical and physical processes in structured soils.
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Affiliation(s)
- Steffen Schlüter
- Department Soil System Sciences , Helmholtz-Centre for Environmental Research - UFZ , Halle , Germany
| | - Thilo Eickhorst
- FB 2 (Biology/Chemistry) , University of Bremen , Bremen , Germany
| | - Carsten W Mueller
- TU Munich , Chair of Soil Science , Freising-Weihenstephan , Germany
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29
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Lin AY, Ding Y, Vanselow DJ, Katz SR, Yakovlev MA, Clark DP, Mandrell D, Copper JE, van Rossum DB, Cheng KC. Rigid Embedding of Fixed and Stained, Whole, Millimeter-Scale Specimens for Section-free 3D Histology by Micro-Computed Tomography. J Vis Exp 2018. [PMID: 30394379 PMCID: PMC6235553 DOI: 10.3791/58293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
For over a hundred years, the histological study of tissues has been the gold standard for medical diagnosis because histology allows all cell types in every tissue to be identified and characterized. Our laboratory is actively working to make technological advances in X-ray micro-computed tomography (micro-CT) that will bring the diagnostic power of histology to the study of full tissue volumes at cellular resolution (i.e., an X-ray Histo-tomography modality). Toward this end, we have made targeted improvements to the sample preparation pipeline. One key optimization, and the focus of the present work, is a straightforward method for rigid embedding of fixed and stained millimeter-scale samples. Many of the published methods for sample immobilization and correlative micro-CT imaging rely on placing the samples in paraffin wax, agarose, or liquids such as alcohol. Our approach extends this work with custom procedures and the design of a 3-dimensional printable apparatus to embed the samples in an acrylic resin directly into polyimide tubing, which is relatively transparent to X-rays. Herein, sample preparation procedures are described for the samples from 0.5 to 10 mm in diameter, which would be suitable for whole zebrafish larvae and juveniles, or other animals and tissue samples of similar dimensions. As proof of concept, we have embedded the specimens from Danio, Drosophila, Daphnia, and a mouse embryo; representative images from 3-dimensional scans for three of these samples are shown. Importantly, our methodology leads to multiple benefits including rigid immobilization, long-term preservation of laboriously-created resources, and the ability to re-interrogate samples.
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Affiliation(s)
- Alex Y Lin
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine; Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine
| | - Yifu Ding
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine; Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine; Medical Scientist Training Program, Penn State College of Medicine
| | - Daniel J Vanselow
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine; Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine
| | - Spencer R Katz
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine; Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine; Medical Scientist Training Program, Penn State College of Medicine
| | - Maksim A Yakovlev
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine; Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine
| | - Darin P Clark
- Center for In Vivo Microscopy, Duke University Medical Center
| | | | - Jean E Copper
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine; Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine
| | - Damian B van Rossum
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine; Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine
| | - Keith C Cheng
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine; Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine;
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30
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Gusmão LC, Grajales A, Rodríguez E. Sea Anemones through X-Rays: Visualization of Two Species ofDiadumene(Cnidaria, Actiniaria) Using Micro-CT. AMERICAN MUSEUM NOVITATES 2018. [DOI: 10.1206/3907.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Luciana C. Gusmão
- Department of Invertebrate Zoology, American Museum of Natural History, New York
| | - Alejandro Grajales
- Department of Invertebrate Zoology, American Museum of Natural History, New York
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Estefania Rodríguez
- Department of Invertebrate Zoology, American Museum of Natural History, New York
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31
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Marcondes Machado F, Passos FD, Giribet G. The use of micro-computed tomography as a minimally invasive tool for anatomical study of bivalves (Mollusca: Bivalvia). Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Fabrizio Marcondes Machado
- Programa de Pós-Graduação em Biologia Animal, Universidade Estadual de Campinas (UNICAMP) CEP, Campinas, SP, Brasil
| | - Flávio Dias Passos
- Programa de Pós-Graduação em Biologia Animal, Universidade Estadual de Campinas (UNICAMP) CEP, Campinas, SP, Brasil
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), CEP, Campinas, SP, Brasil
| | - Gonzalo Giribet
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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32
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Gutiérrez Y, Ott D, Töpperwien M, Salditt T, Scherber C. X-ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation. Ecol Evol 2018; 8:7717-7732. [PMID: 30151184 PMCID: PMC6106166 DOI: 10.1002/ece3.4149] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 04/04/2018] [Accepted: 04/09/2018] [Indexed: 12/15/2022] Open
Abstract
Imaging techniques are a cornerstone of contemporary biology. Over the last decades, advances in microscale imaging techniques have allowed fascinating new insights into cell and tissue morphology and internal anatomy of organisms across kingdoms. However, most studies so far provided snapshots of given reference taxa, describing organs and tissues under "idealized" conditions. Surprisingly, there is an almost complete lack of studies investigating how an organism's internal morphology changes in response to environmental drivers. Consequently, ecology as a scientific discipline has so far almost neglected the possibilities arising from modern microscale imaging techniques. Here, we provide an overview of recent developments of X-ray computed tomography as an affordable, simple method of high spatial resolution, allowing insights into three-dimensional anatomy both in vivo and ex vivo. We review ecological studies using this technique to investigate the three-dimensional internal structure of organisms. In addition, we provide practical comparisons between different preparation techniques for maximum contrast and tissue differentiation. In particular, we consider the novel modality of phase contrast by self-interference of the X-ray wave behind an object (i.e., phase contrast by free space propagation). Using the cricket Acheta domesticus (L.) as model organism, we found that the combination of FAE fixative and iodine staining provided the best results across different tissues. The drying technique also affected contrast and prevented artifacts in specific cases. Overall, we found that for the interests of ecological studies, X-ray computed tomography is useful when the tissue or structure of interest has sufficient contrast that allows for an automatic or semiautomatic segmentation. In particular, we show that reconstruction schemes which exploit phase contrast can yield enhanced image quality. Combined with suitable specimen preparation and automated analysis, X-ray CT can therefore become a promising quantitative 3D imaging technique to study organisms' responses to environmental drivers, in both ecology and evolution.
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Affiliation(s)
| | - David Ott
- Institute of Landscape EcologyUniversity of MünsterMünsterGermany
| | | | - Tim Salditt
- Institute for X‐Ray PhysicsUniversity of GöttingenGöttingenGermany
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33
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Glueckert R, Johnson Chacko L, Schmidbauer D, Potrusil T, Pechriggl EJ, Hoermann R, Brenner E, Reka A, Schrott-Fischer A, Handschuh S. Visualization of the Membranous Labyrinth and Nerve Fiber Pathways in Human and Animal Inner Ears Using MicroCT Imaging. Front Neurosci 2018; 12:501. [PMID: 30108474 PMCID: PMC6079228 DOI: 10.3389/fnins.2018.00501] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 07/03/2018] [Indexed: 12/18/2022] Open
Abstract
Design and implantation of bionic implants for restoring impaired hair cell function relies on accurate knowledge about the microanatomy and nerve fiber pathways of the human inner ear and its variation. Non-destructive isotropic imaging of soft tissues of the inner ear with lab-based microscopic X-ray computed tomography (microCT) offers high resolution but requires contrast enhancement using compounds with high X-ray attenuation. We evaluated different contrast enhancement techniques in mice, cat, and human temporal bones to differentially visualize the membranous labyrinth, sensory epithelia, and their innervating nerves together with the facial nerve and middle ear. Lugol’s iodine potassium iodine (I2KI) gave high soft tissue contrast in ossified specimens but failed to provide unambiguous identification of smaller nerve fiber bundles inside small bony canals. Fixation or post-fixation with osmium tetroxide followed by decalcification in EDTA provided superior contrast for nerve fibers and membranous structures. We processed 50 human temporal bones and acquired microCT scans with 15 μm voxel size. Subsequently we segmented sensorineural structures and the endolymphatic compartment for 3D representations to serve for morphometric variation analysis. We tested higher resolution image acquisition down to 3.0 μm voxel size in human and 0.5 μm in mice, which provided a unique level of detail and enabled us to visualize single neurons and hair cells in the mouse inner ear, which could offer an alternative quantitative analysis of cell numbers in smaller animals. Bigger ossified human temporal bones comprising the middle ear and mastoid bone can be contrasted with I2KI and imaged in toto at 25 μm voxel size. These data are suitable for surgical planning for electrode prototype placements. A preliminary assessment of geometric changes through tissue processing resulted in 1.6% volume increase caused during decalcification by EDTA and 0.5% volume increase caused by partial dehydration to 70% ethanol, which proved to be the best mounting medium for microCT image acquisition.
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Affiliation(s)
- Rudolf Glueckert
- Department of Otolaryngology, Medical University of Innsbruck, Innsbruck, Austria.,University Clinics Innsbruck, Tirol Kliniken, University Clinic for Ear, Nose and Throat Medicine Innsbruck, Innsbruck, Austria
| | - Lejo Johnson Chacko
- Department of Otolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Schmidbauer
- Department of Otolaryngology, Medical University of Innsbruck, Innsbruck, Austria.,Department of Biotechnology and Food Engineering, Management Center Innsbruck (MCI), Innsbruck, Austria
| | - Thomas Potrusil
- Department of Otolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Elisabeth J Pechriggl
- Department of Anatomy, Histology and Embryology, Division of Clinical and Functional Anatomy, Medical University of Innsbruck, Innsbruck, Austria
| | - Romed Hoermann
- Department of Anatomy, Histology and Embryology, Division of Clinical and Functional Anatomy, Medical University of Innsbruck, Innsbruck, Austria
| | - Erich Brenner
- Department of Anatomy, Histology and Embryology, Division of Clinical and Functional Anatomy, Medical University of Innsbruck, Innsbruck, Austria
| | - Alen Reka
- Department of Otolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Stephan Handschuh
- VetImaging, VetCore Facility for Research, University of Veterinary Medicine, Vienna, Austria
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34
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Nischik ES, Krieger J. Evaluation of standard imaging techniques and volumetric preservation of nervous tissue in genetically identical offspring of the crayfish Procambarus fallax cf. virginalis (Marmorkrebs). PeerJ 2018; 6:e5181. [PMID: 30018856 PMCID: PMC6044273 DOI: 10.7717/peerj.5181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 06/18/2018] [Indexed: 01/24/2023] Open
Abstract
In the field of comparative neuroanatomy, a meaningful interspecific comparison demands quantitative data referring to method-specific artifacts. For evaluating the potential of state-of-the-art imaging techniques in arthropod neuroanatomy, micro-computed X-ray microscopy (μCT) and two different approaches using confocal laser-scanning microscopy (cLSM) were applied to obtain volumetric data of the brain and selected neuropils in Procambarus fallax forma virginalis (Crustacea, Malacostraca, Decapoda). The marbled crayfish P. fallax cf. virginalis features a parthogenetic reproduction generating genetically identical offspring from unfertilized eggs. Therefore, the studied organism provides ideal conditions for the comparative analysis of neuroanatomical imaging techniques and the effect of preceding sample preparations of nervous tissue. We found that wet scanning of whole animals conducted with μCT turned out to be the least disruptive method. However, in an additional experiment it was discovered that fixation in Bouin’s solution, required for μCT scans, resulted in an average tissue shrinkage of 24% compared to freshly dissected and unfixed brains. The complete sample preparation using fixation in half-strength Karnovsky’s solution of dissected brains led to an additional volume decrease of 12.5%, whereas the preparation using zinc-formaldehyde as fixative resulted in a shrinkage of 5% in comparison to the volumes obtained by μCT. By minimizing individual variability, at least for aquatic arthropods, this pioneer study aims for the inference of method-based conversion factors in the future, providing a valuable tool for reducing quantitative neuroanatomical data already published to a common denominator. However, volumetric deviations could be shown for all experimental protocols due to methodological noise and/or phenotypic plasticity among genetically identical individuals. MicroCT using undried tissue is an appropriate non-disruptive technique for allometry of arthropod brains since spatial organ relationships are conserved and tissue shrinkage is minimized. Collecting tissue-based shrinkage factors according to specific sample preparations might allow a better comparability of volumetric data from the literature, even if another technique was applied.
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Affiliation(s)
- Emanuel S Nischik
- Zoological Institute and Museum, Cytology and Evolutionary Biology, University of Greifswald, Greifswald, Germany
| | - Jakob Krieger
- Zoological Institute and Museum, Cytology and Evolutionary Biology, University of Greifswald, Greifswald, Germany
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35
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van den Boogert T, van Hoof M, Handschuh S, Glueckert R, Guinand N, Guyot JP, Kingma H, Perez-Fornos A, Seppen B, Johnson Chacko L, Schrott-Fischer A, van de Berg R. Optimization of 3D-Visualization of Micro-Anatomical Structures of the Human Inner Ear in Osmium Tetroxide Contrast Enhanced Micro-CT Scans. Front Neuroanat 2018; 12:41. [PMID: 29872380 PMCID: PMC5972190 DOI: 10.3389/fnana.2018.00041] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/27/2018] [Indexed: 11/30/2022] Open
Abstract
Introduction: Knowledge of the neuro-anatomical architecture of the inner ear contributes to the improvement and development of cochlear and vestibular implants. The present knowledge is mainly based on two-dimensional images (histology) or derived models that simplify the complexity of this architecture. This study investigated the feasibility of visualizing relevant neuro-anatomical structures of the inner ear in a dynamic three-dimensional reproduction, using a combination of staining, micro-CT imaging and an image processing algorithm. Methods: Four fresh cadaveric temporal bones were postfixed with osmium tetroxide (OsO4) and decalcified with EDTA. Micro-CT was used for scanning at 10 μm (4 scans) and 5.5 μm (1 scan) voxel resolution. A new image processing algorithm was developed and the scans were visualized in open source software. Results: OsO4 enhanced the contrast in all scans and the visualization was substantially improved by the image processing algorithm. The three-dimensional renderings provided detailed visualization of the whole inner ear. Details were visible up to the size of individual neurons, nerve crossings and the specific neuro-anatomical structures such as the tunnel of Corti. Conclusion: The combination of OsO4, micro-CT and the proposed image processing algorithm provides an accurate and detailed visualization of the three-dimensional micro-anatomy of the human inner ear.
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Affiliation(s)
- Thomas van den Boogert
- Division of Balance Disorders, Department of Otorhinolaryngology, Head, and Neck Surgery, Faculty of Health Medicine and Life Sciences, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Marc van Hoof
- Division of Balance Disorders, Department of Otorhinolaryngology, Head, and Neck Surgery, Faculty of Health Medicine and Life Sciences, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Stephan Handschuh
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Rudolf Glueckert
- Department of Otorhinolaryngology, Medical University Innsbruck, Innsbruck, Austria
| | - Nils Guinand
- Department of Clinical Neurosciences, Service of Otorhinolaryngology, Head, and Neck Surgery, Geneva University Hospitals, Geneva, Switzerland
| | - Jean-Philippe Guyot
- Department of Clinical Neurosciences, Service of Otorhinolaryngology, Head, and Neck Surgery, Geneva University Hospitals, Geneva, Switzerland
| | - Herman Kingma
- Division of Balance Disorders, Department of Otorhinolaryngology, Head, and Neck Surgery, Faculty of Health Medicine and Life Sciences, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, Netherlands
- Vestibular Laboratory, Faculty of Physics, Tomsk State National Research University, Tomsk, Russia
| | - Angelica Perez-Fornos
- Department of Clinical Neurosciences, Service of Otorhinolaryngology, Head, and Neck Surgery, Geneva University Hospitals, Geneva, Switzerland
| | - Bart Seppen
- Division of Balance Disorders, Department of Otorhinolaryngology, Head, and Neck Surgery, Faculty of Health Medicine and Life Sciences, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Lejo Johnson Chacko
- Department of Otorhinolaryngology, Medical University Innsbruck, Innsbruck, Austria
| | | | - Raymond van de Berg
- Division of Balance Disorders, Department of Otorhinolaryngology, Head, and Neck Surgery, Faculty of Health Medicine and Life Sciences, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, Netherlands
- Vestibular Laboratory, Faculty of Physics, Tomsk State National Research University, Tomsk, Russia
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36
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Katchalski T, Case T, Kim KY, Ramachandra R, Bushong EA, Deerinck TJ, Haberl MG, Mackey MR, Peltier S, Castillon GA, Fujikawa N, Lawrence AR, Ellisman MH. Iron-specific Signal Separation from within Heavy Metal Stained Biological Samples Using X-Ray Microtomography with Polychromatic Source and Energy-Integrating Detectors. Sci Rep 2018; 8:7553. [PMID: 29765060 PMCID: PMC5953933 DOI: 10.1038/s41598-018-25099-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 04/12/2018] [Indexed: 11/09/2022] Open
Abstract
Biological samples are frequently stained with heavy metals in preparation for examining the macro, micro and ultra-structure using X-ray microtomography and electron microscopy. A single X-ray microtomography scan reveals detailed 3D structure based on staining density, yet it lacks both material composition and functional information. Using a commercially available polychromatic X-ray source, energy integrating detectors and a two-scan configuration labelled by their energy- "High" and "Low", we demonstrate how a specific element, here shown with iron, can be detected from a mixture with other heavy metals. With proper selection of scan configuration, achieving strong overlap of source characteristic emission lines and iron K-edge absorption, iron absorption was enhanced enabling K-edge imaging. Specifically, iron images were obtained by scatter plot material analysis, after selecting specific regions within scatter plots generated from the "High" and "Low" scans. Using this method, we identified iron rich regions associated with an iron staining reaction that marks the nodes of Ranvier along nerve axons within mouse spinal roots, also stained with osmium metal commonly used for electron microscopy.
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Affiliation(s)
- Tsvi Katchalski
- National Center for Microscopy and Imaging Research (NCMIR), University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA.
| | - Tom Case
- Carl Zeiss X-Ray Microscopy, 4385 Hopyard Road, Suite 100, Pleasanton, CA, 94588, USA
| | - Keun-Young Kim
- National Center for Microscopy and Imaging Research (NCMIR), University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA
| | - Ranjan Ramachandra
- National Center for Microscopy and Imaging Research (NCMIR), University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA
| | - Eric A Bushong
- National Center for Microscopy and Imaging Research (NCMIR), University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research (NCMIR), University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA
| | - Matthias G Haberl
- National Center for Microscopy and Imaging Research (NCMIR), University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA
| | - Mason R Mackey
- National Center for Microscopy and Imaging Research (NCMIR), University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA
| | - Steven Peltier
- National Center for Microscopy and Imaging Research (NCMIR), University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA
| | - Guillaume A Castillon
- National Center for Microscopy and Imaging Research (NCMIR), University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA
| | - Nobuko Fujikawa
- Carl Zeiss X-Ray Microscopy, 4385 Hopyard Road, Suite 100, Pleasanton, CA, 94588, USA
| | - Albert R Lawrence
- National Center for Microscopy and Imaging Research (NCMIR), University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research (NCMIR), University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA. .,Departments of Neurosciences and Bioengineering, University of California San Diego, 9500 Gilman Dr. MC 0608, La Jolla, CA, 92093-0608, USA.
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37
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Abstract
Emily Baird and Gavin Taylor describe how you can make three-dimensional models of biological samples using x-ray micro-computed tomography.
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Affiliation(s)
- Emily Baird
- Department of Biology, Lund University, Lund 223 62, Sweden.
| | - Gavin Taylor
- Department of Biology, Lund University, Lund 223 62, Sweden.
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38
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Schwaha T. Morphology and ontogeny of Lophopus crystallinus lophophore support the epistome as ancestral character of phylactolaemate bryozoans. ZOOMORPHOLOGY 2018; 137:355-366. [PMID: 30174370 PMCID: PMC6105306 DOI: 10.1007/s00435-018-0402-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/05/2018] [Accepted: 03/08/2018] [Indexed: 02/04/2023]
Abstract
Phylactolaemate bryozoans are the sister-group to all remaining bryozoan taxa. Consequently, their study is essential to reveal and analyze ancestral traits of Phylactolaemata and Bryozoa in general. They are the only bryozoans to possess an epistome which traditionally has been regarded as shared with phoronids and brachiopods. Contrary to older observations, an epistome was recently reported to be missing in the early branching phylactolaemate Lophopus crystallinus. In this study, the ontogeny of the lophophoral base and also its three-dimensional structure in adult specimens was reinvestigated to assess whether an epistome is never formed during ontogeny and absent in adult specimens. The results show that organogenesis during the budding process in this species is similar to other, previously investigated, species. The epistome anlage in L. crystallinus forms in early buds from the outer budding layer which penetrates the two shanks of the u-shaped gut. This ingression of the epithelium further proceeds distally and starts to wrap over the forming ganglion. The adult epistome is a rather short, but present bulge above the cerebral ganglion with prominent muscle bundles traversing its cavity. Distally it is arched by the forked canal that in L. crystallinus has a particularly thick and prominent epithelium in the three median tentacles. This study shows that neither during ontogeny nor in the adult stage an epistome is absent. The epistome is less pronounced than in other phylactolaemates, but otherwise similar in its general structure. Consequently, an epistome can be assumed to be present in the ground pattern of Phylactolaemata.
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Affiliation(s)
- Thomas Schwaha
- Department Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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39
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Jahn H, Oliveira IDES, Gross V, Martin C, Hipp A, Mayer G, Hammel JU. Evaluation of contrasting techniques for X-ray imaging of velvet worms (Onychophora). J Microsc 2018; 270:343-358. [PMID: 29469207 DOI: 10.1111/jmi.12688] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 12/20/2017] [Accepted: 01/29/2018] [Indexed: 01/04/2023]
Abstract
Non-invasive imaging techniques like X-ray computed tomography have become very popular in zoology, as they allow for simultaneous imaging of the internal and external morphology of organisms. Nevertheless, the effect of different staining approaches required for this method on samples lacking mineralized tissues, such as soft-bodied invertebrates, remains understudied. Herein, we used synchrotron radiation-based X-ray micro-computed tomography to compare the effects of commonly used contrasting approaches on onychophorans - soft-bodied invertebrates important for studying animal evolution. Representatives of Euperipatoides rowelli were stained with osmium tetroxide (vapour or solution), ruthenium red, phosphotungstic acid, or iodine. Unstained specimens were imaged using both standard attenuation-based and differential phase-contrast setups to simulate analyses with museum material. Our comparative qualitative analyses of several tissue types demonstrate that osmium tetroxide provides the best overall tissue contrast in onychophorans, whereas the remaining staining agents rather favour the visualisation of specific tissues and/or structures. Quantitative analyses using signal-to-noise ratio measurements show that the level of image noise may vary according to the staining agent and scanning medium selected. Furthermore, box-and-whisker plots revealed substantial overlap in grey values among structures in all datasets, suggesting that a combination of semiautomatic and manual segmentation of structures is required for comprehensive 3D reconstructions of Onychophora, irrespective of the approach selected. Our results show that X-ray micro-computed tomography is a promising technique for studying onychophorans and, despite the benefits and disadvantages of different staining agents for specific tissues/structures, this method retrieves informative data that may eventually help address evolutionary questions long associated with Onychophora.
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Affiliation(s)
- Henry Jahn
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Ivo DE Sena Oliveira
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany.,Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vladimir Gross
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Christine Martin
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Alexander Hipp
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Geesthacht, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Jörg U Hammel
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Geesthacht, Germany.,Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-University of Jena, Jena, Germany
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40
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Oláh T, Reinhard J, Gao L, Goebel LKH, Madry H. Reliable landmarks for precise topographical analyses of pathological structural changes of the ovine tibial plateau in 2-D and 3-D subspaces. Sci Rep 2018; 8:75. [PMID: 29311696 PMCID: PMC5758565 DOI: 10.1038/s41598-017-18426-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 12/06/2017] [Indexed: 11/09/2022] Open
Abstract
Selecting identical topographical locations to analyse pathological structural changes of the osteochondral unit in translational models remains difficult. The specific aim of the study was to provide objectively defined reference points on the ovine tibial plateau based on 2-D sections of micro-CT images useful for reproducible sample harvesting and as standardized landmarks for landmark-based 3-D image registration. We propose 5 reference points, 11 reference lines and 12 subregions that are detectable macroscopically and on 2-D micro-CT sections. Their value was confirmed applying landmark-based rigid and affine 3-D registration methods. Intra- and interobserver comparison showed high reliabilities, and constant positions (standard errors < 1%). Spatial patterns of the thicknesses of the articular cartilage and subchondral bone plate were revealed by measurements in 96 individual points of the tibial plateau. As a case study, pathological phenomena 6 months following OA induction in vivo such as osteophytes and areas of OA development were mapped to the individual subregions. These new reference points and subregions are directly identifiable on tibial plateau specimens or macroscopic images, enabling a precise topographical location of pathological structural changes of the osteochondral unit in both 2-D and 3-D subspaces in a region-appropriate fashion relevant for translational investigations.
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Affiliation(s)
- Tamás Oláh
- Center of Experimental Orthopaedics, Saarland University, Homburg, Germany
| | - Jan Reinhard
- Center of Experimental Orthopaedics, Saarland University, Homburg, Germany
| | - Liang Gao
- Center of Experimental Orthopaedics, Saarland University, Homburg, Germany
| | - Lars K H Goebel
- Center of Experimental Orthopaedics, Saarland University, Homburg, Germany.,Department of Orthopaedic Surgery, Saarland University Medical Center, Homburg, Germany
| | - Henning Madry
- Center of Experimental Orthopaedics, Saarland University, Homburg, Germany. .,Department of Orthopaedic Surgery, Saarland University Medical Center, Homburg, Germany.
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41
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Abstract
X-ray micro-computed tomography (μCT) is a technique which can obtain three-dimensional images of a sample, including its internal structure, without the need for destructive sectioning. Here, we review the capability of the technique and examine its potential to provide novel insights into the lifestyles of parasites embedded within host tissue. The current capabilities and limitations of the technology in producing contrast in soft tissues are discussed, as well as the potential solutions for parasitologists looking to apply this technique. We present example images of the mouse whipworm Trichuris muris and discuss the application of μCT to provide unique insights into parasite behaviour and pathology, which are inaccessible to other imaging modalities.
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42
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A simple setup for episcopic microtomy and a digital image processing workflow to acquire high-quality volume data and 3D surface models of small vertebrates. ZOOMORPHOLOGY 2017. [DOI: 10.1007/s00435-017-0386-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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43
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Ribi W, Zeil J. Three-dimensional visualization of ocellar interneurons of the orchid beeEuglossa imperialisusing micro X-ray computed tomography. J Comp Neurol 2017; 525:3581-3595. [PMID: 28608425 DOI: 10.1002/cne.24260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/07/2017] [Accepted: 05/09/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Willi Ribi
- Research School of Biology, The Australian National University; Canberra Australian Capital Territory Australia
| | - Jochen Zeil
- Research School of Biology, The Australian National University; Canberra Australian Capital Territory Australia
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44
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Rico-Guevara A. Relating form to function in the hummingbird feeding apparatus. PeerJ 2017; 5:e3449. [PMID: 28607842 PMCID: PMC5466813 DOI: 10.7717/peerj.3449] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/19/2017] [Indexed: 01/03/2023] Open
Abstract
A complete understanding of the feeding structures is fundamental in order to study how animals survive. Some birds use long and protrusible tongues as the main tool to collect their central caloric source (e.g., woodpeckers and nectarivores). Hummingbirds are the oldest and most diverse clade of nectarivorous vertebrates, being a perfect subject to study tongue specializations. Their tongue functions to intraorally transport arthropods through their long bills and enables them to exploit the nectarivorous niche by collecting small amounts of liquid, therefore it is of vital importance to study its anatomy and structure at various scales. I focused on the portions of the hummingbird tongue that have been shown to be key for understanding their feeding mechanisms. I used histology, transmission and scanning electron microscopy, microCT, and ex-vivo experiments in order to advance the comprehension of the morphology and functioning of the hummingbird feeding apparatus. I found that hummingbird tongues are composed mainly of thin cornified epithelium, lack papillae, and completely fill the internal cast of the rostral oropharyngeal cavity. Understanding this puzzle-piece match between bill and tongue will be essential for the study of intraoral transport of nectar. Likewise, I found that the structural composition and tissue architecture of the tongue groove walls provide the rostral portion of the tongue with elastic properties that are central to the study of tongue-nectar interactions during the feeding process. Detailed studies on hummingbirds set the basis for comparisons with other nectar-feeding birds and contribute to comprehend the natural solutions to collecting liquids in the most efficient way possible.
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Affiliation(s)
- Alejandro Rico-Guevara
- Department of Integrative Biology, University of California, Berkeley, CA, United States of America
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45
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Parlanti P, Cappello V, Brun F, Tromba G, Rigolio R, Tonazzini I, Cecchini M, Piazza V, Gemmi M. Size and specimen-dependent strategy for x-ray micro-ct and tem correlative analysis of nervous system samples. Sci Rep 2017; 7:2858. [PMID: 28588216 PMCID: PMC5460131 DOI: 10.1038/s41598-017-02998-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/30/2017] [Indexed: 11/08/2022] Open
Abstract
Correlative approaches are a powerful tool in the investigation of biological samples, but require specific preparation procedures to maintain the strength of the employed methods. Here we report the optimization of the embedding protocol of nervous system samples for a correlative synchrotron X-ray computed microtomography (micro-CT) and transmission electron microscopy (TEM) approach. We demonstrate that it is possible to locate, with the micrometric resolution of micro-CT, specific volumes of interest for a further ultrastructural characterization to be performed with TEM. This approach can be applied to samples of different size and morphology up to several cm. Our optimized method represents an invaluable tool for investigating those pathologies in which microscopic alterations are localized in few confined regions, rather than diffused in entire tissues, organs or systems. We present a proof of concept of our method in a mouse model of Globoid Cells Leukodistrophy.
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Affiliation(s)
- P Parlanti
- NEST, Scuola Normale Superiore, Piazza San Silvestro 12, I-56127, Pisa, Italy
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, I-56127, Pisa, Italy
| | - V Cappello
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, I-56127, Pisa, Italy.
| | - F Brun
- National Research Council - Institute of Nanotechnology (CNR Nanotech) c/o Dipartimento di Fisica, Università Sapienza, Piazzale Aldo Moro 5, I-00185, Rome, Italy
- Dipartimento di Ingegneria e Architettura, Università degli Studi di Trieste, Via A. Valerio 10, I-34127, Trieste, Italy
- Elettra - Sincrotrone Trieste S.C.p.A., S.S. 14 km 163.5 in Area Science Park, I-34149, Basovizza, Trieste, Italy
| | - G Tromba
- Elettra - Sincrotrone Trieste S.C.p.A., S.S. 14 km 163.5 in Area Science Park, I-34149, Basovizza, Trieste, Italy
| | - R Rigolio
- Dipartimento di Medicina e Chirurgia, Experimental Neurology Unit, Università degli Studi di Milano-Bicocca, Via Cadore 48, I-20900, Monza, Italy
| | - I Tonazzini
- NEST, Scuola Normale Superiore and Istituto di Nanoscienze - CNR, Piazza San Silvestro 12, I-56127, Pisa, Italy
- Fondazione Umberto Veronesi, Piazza Velasca, I-20122, Milano, Italy
| | - M Cecchini
- NEST, Scuola Normale Superiore and Istituto di Nanoscienze - CNR, Piazza San Silvestro 12, I-56127, Pisa, Italy
| | - V Piazza
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, I-56127, Pisa, Italy
| | - M Gemmi
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, I-56127, Pisa, Italy
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46
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Janel S, Werkmeister E, Bongiovanni A, Lafont F, Barois N. CLAFEM: Correlative light atomic force electron microscopy. Methods Cell Biol 2017; 140:165-185. [PMID: 28528632 DOI: 10.1016/bs.mcb.2017.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Atomic force microscopy (AFM) is becoming increasingly used in the biology field. It can give highly accurate topography and biomechanical quantitative data, such as adhesion, elasticity, and viscosity, on living samples. Nowadays, correlative light electron microscopy is a must-have tool in the biology field that combines different microscopy techniques to spatially and temporally analyze the structure and function of a single sample. Here, we describe the combination of AFM with superresolution light microscopy and electron microscopy. We named this technique correlative light atomic force electron microscopy (CLAFEM) in which AFM can be used on fixed and living cells in association with superresolution light microscopy and further processed for transmission or scanning electron microscopy. We herein illustrate this approach to observe cellular bacterial infection and cytoskeleton. We show that CLAFEM brings complementary information at the cellular level, from on the one hand protein distribution and topography at the nanometer scale and on the other hand elasticity at the piconewton scales to fine ultrastructural details.
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Affiliation(s)
- Sébastien Janel
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Elisabeth Werkmeister
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Antonino Bongiovanni
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Frank Lafont
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Nicolas Barois
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
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47
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Handschuh S, Beisser CJ, Ruthensteiner B, Metscher BD. Microscopic dual-energy CT (microDECT): a flexible tool for multichannel ex vivo 3D imaging of biological specimens. J Microsc 2017; 267:3-26. [PMID: 28267884 DOI: 10.1111/jmi.12543] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/28/2017] [Accepted: 01/29/2017] [Indexed: 12/19/2022]
Abstract
Dual-energy computed tomography (DECT) uses two different x-ray energy spectra in order to differentiate between tissues, materials or elements in a single sample or patient. DECT is becoming increasingly popular in clinical imaging and preclinical in vivo imaging of small animal models, but there have been only very few reports on ex vivo DECT of biological samples at microscopic resolutions. The present study has three main aims. First, we explore the potential of microscopic DECT (microDECT) for delivering isotropic multichannel 3D images of fixed biological samples with standard commercial laboratory-based microCT setups at spatial resolutions reaching below 10 μm. Second, we aim for retaining the maximum image resolution and quality during the material decomposition. Third, we want to test the suitability for microDECT imaging of different contrast agents currently used for ex vivo staining of biological samples. To address these aims, we used microCT scans of four different samples stained with x-ray dense contrast agents. MicroDECT scans were acquired with five different commercial microCT scanners from four companies. We present a detailed description of the microDECT workflow, including sample preparation, image acquisition, image processing and postreconstruction material decomposition, which may serve as practical guide for applying microDECT. The MATLAB script (The Mathworks Inc., Natick, MA, USA) used for material decomposition (including a graphical user interface) is provided as a supplement to this paper (https://github.com/microDECT/DECTDec). In general, the presented microDECT workflow yielded satisfactory results for all tested specimens. Original scan resolutions have been mostly retained in the separate material fractions after basis material decomposition. In addition to decomposition of mineralized tissues (inherent sample contrast) and stained soft tissues, we present a case of double labelling of different soft tissues with subsequent material decomposition. We conclude that, in contrast to in vivo DECT examinations, small ex vivo specimens offer some clear advantages regarding technical parameters of the microCT setup and the use of contrast agents. These include a higher flexibility in source peak voltages and x-ray filters, a lower degree of beam hardening due to small sample size, the lack of restriction to nontoxic contrast agents and the lack of a limit in exposure time and radiation dose. We argue that microDECT, because of its flexibility combined with already established contrast agents and the vast number of currently unexploited stains, will in future represent an important technique for various applications in biological research.
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Affiliation(s)
- S Handschuh
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria.,Department of Theoretical Biology, University of Vienna, Vienna, Austria
| | - C J Beisser
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | | | - B D Metscher
- Department of Theoretical Biology, University of Vienna, Vienna, Austria
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48
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Karreman MA, Ruthensteiner B, Mercier L, Schieber NL, Solecki G, Winkler F, Goetz JG, Schwab Y. Find your way with X-Ray. Methods Cell Biol 2017; 140:277-301. [DOI: 10.1016/bs.mcb.2017.03.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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49
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Wipfler B, Pohl H, Yavorskaya MI, Beutel RG. A review of methods for analysing insect structures - the role of morphology in the age of phylogenomics. CURRENT OPINION IN INSECT SCIENCE 2016; 18:60-68. [PMID: 27939712 DOI: 10.1016/j.cois.2016.09.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Techniques currently used in insect morphology are outlined briefly. Scanning electron microscopy (SEM) and microphotography are used mainly for documenting external features, the former providing more information on tiny surface structures and the latter on coloration, transparency and degree of sclerotization. A broad spectrum of methods is now available for anatomical studies: histological serial sections, confocal laser scanning microscopy (CLSM), light-sheet fluorescence microscopy (LSFM), serial block-face scanning electron microscopy (SBFSEM), dual beam scanning electron microscopy (FIB-SEM), nuclear magnetic resonance imaging (NMRI), and μ-computed tomography (micro-CT). The use of SBFSEM and FIB-SEM is restricted to extremely small samples. NMRI is used mainly in in vivo studies. Micro-computed tomography, in combination with computer-based reconstruction, has greatly accelerated the acquisition of high quality data in a phylogenetic context. Morphology will continue to play a vital role in phylogenetic and evolutionary investigations. It provides independent data for checking the plausibility of molecular phylogenies and is the only source of information for placing extinct taxa. It is the necessary basis for reconstructing character evolution on the phenotypic level and for developing complex evolutionary scenarios. Computer-based anatomical ontologies are an additional future perspective of morphological work.
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Affiliation(s)
- Benjamin Wipfler
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Hans Pohl
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Margarita I Yavorskaya
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Rolf G Beutel
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany.
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50
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Shami GJ, Cheng D, Huynh M, Vreuls C, Wisse E, Braet F. 3-D EM exploration of the hepatic microarchitecture - lessons learned from large-volume in situ serial sectioning. Sci Rep 2016; 6:36744. [PMID: 27834401 PMCID: PMC5105151 DOI: 10.1038/srep36744] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/20/2016] [Indexed: 12/12/2022] Open
Abstract
To-date serial block-face scanning electron microscopy (SBF-SEM) dominates as the premier technique for generating three-dimensional (3-D) data of resin-embedded biological samples at an unprecedented depth volume. Given the infancy of the technique, limited literature is currently available regarding the applicability of SBF-SEM for the ultrastructural investigation of tissues. Herein, we provide a comprehensive and rigorous appraisal of five different SBF-SEM sample preparation protocols for the large-volume exploration of the hepatic microarchitecture at an unparalleled X, Y and Z resolution. In so doing, we qualitatively and quantitatively validate the use of a comprehensive SBF-SEM sample preparation protocol, based on the application of heavy metal fixatives, stains and mordanting agents. Employing the best-tested SBF-SEM approach, enabled us to assess large-volume morphometric data on murine parenchymal cells, sinusoids and bile canaliculi. Finally, we integrated the validated SBF-SEM protocol with a correlative light and electron microscopy (CLEM) approach. The combination of confocal scanning laser microscopy and SBF-SEM provided a novel way to picture subcellular detail. We appreciate that this multidimensional approach will aid the subsequent research of liver tissue under relevant experimental and disease conditions.
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Affiliation(s)
- Gerald John Shami
- School of Medical Sciences (Discipline of Anatomy and Histology) – The Bosch Institute, The University of Sydney, NSW 2006, Australia
| | - Delfine Cheng
- School of Medical Sciences (Discipline of Anatomy and Histology) – The Bosch Institute, The University of Sydney, NSW 2006, Australia
| | - Minh Huynh
- Australian Centre for Microscopy and Microanalysis (ACMM), The University of Sydney, NSW 2006, Australia
| | - Celien Vreuls
- Department of Pathology, Amphia Hospital, Breda, The Netherlands
| | - Eddie Wisse
- Australian Centre for Microscopy and Microanalysis (ACMM), The University of Sydney, NSW 2006, Australia
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, University of Maastricht, 6200 MD Maastricht, The Netherlands
- Department of Internal Medicine, University of Maastricht, 6200, MD Maastricht, The Netherlands
| | - Filip Braet
- School of Medical Sciences (Discipline of Anatomy and Histology) – The Bosch Institute, The University of Sydney, NSW 2006, Australia
- Australian Centre for Microscopy and Microanalysis (ACMM), The University of Sydney, NSW 2006, Australia
- Cellular Imaging Facility, Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
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