1
|
Sinclair R, Wang M, Jawaid MZ, Longkumer T, Aaron J, Rossetti B, Wait E, McDonald K, Cox D, Heddleston J, Wilkop T, Drakakaki G. Four-dimensional quantitative analysis of cell plate development in Arabidopsis using lattice light sheet microscopy identifies robust transition points between growth phases. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2829-2847. [PMID: 38436428 DOI: 10.1093/jxb/erae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Cell plate formation during cytokinesis entails multiple stages occurring concurrently and requiring orchestrated vesicle delivery, membrane remodelling, and timely deposition of polysaccharides, such as callose. Understanding such a dynamic process requires dissection in time and space; this has been a major hurdle in studying cytokinesis. Using lattice light sheet microscopy (LLSM), we studied cell plate development in four dimensions, through the behavior of yellow fluorescent protein (YFP)-tagged cytokinesis-specific GTPase RABA2a vesicles. We monitored the entire duration of cell plate development, from its first emergence, with the aid of YFP-RABA2a, in both the presence and absence of cytokinetic callose. By developing a robust cytokinetic vesicle volume analysis pipeline, we identified distinct behavioral patterns, allowing the identification of three easily trackable cell plate developmental phases. Notably, the phase transition between phase I and phase II is striking, indicating a switch from membrane accumulation to the recycling of excess membrane material. We interrogated the role of callose using pharmacological inhibition with LLSM and electron microscopy. Loss of callose inhibited the phase transitions, establishing the critical role and timing of the polysaccharide deposition in cell plate expansion and maturation. This study exemplifies the power of combining LLSM with quantitative analysis to decode and untangle such a complex process.
Collapse
Affiliation(s)
- Rosalie Sinclair
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Minmin Wang
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Muhammad Zaki Jawaid
- Department of Physics and Astronomy, University of California Davis, Davis, CA, USA
| | | | | | | | - Eric Wait
- Janelia Research Campus, Ashburn, VA, USA
| | - Kent McDonald
- Electron Microscope Laboratory, University of California, Berkeley, CA, USA
| | - Daniel Cox
- Department of Physics and Astronomy, University of California Davis, Davis, CA, USA
| | | | - Thomas Wilkop
- Department of Molecular and Cellular Biology, Light Microscopy Imaging Facility, University of California Davis, Davis, CA, USA
| | - Georgia Drakakaki
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| |
Collapse
|
2
|
Sui X, Kuang D, Liu G, Ding Y, Meng M, Xi R. Highly focused beam generated with a height tuned micro-optical structure for high contrast microscopic imaging. OPTICS EXPRESS 2024; 32:19308-19318. [PMID: 38859068 DOI: 10.1364/oe.523606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/04/2024] [Indexed: 06/12/2024]
Abstract
Light sheet illumination technology improves the signal-to-noise ratio, resolution, and reduces scattered backgrounds for biological microscopic detection system. Here, we developed a novel micro-optical structure to produce a focused and uniform beam for the enhancement of imaging contrast. The beam intensity and working distance can be modified by adjusting the height and period of the structure. Our experiments successfully recorded structured light illumination, demonstrating the ability of the structure to capture high-contrast imaging data. We compared the light fields generated with and without the structure to assess the imaging quality, revealing a maximum 4.78-fold improvement in the signal-to-noise ratio. This work provides a potential method for high-resolution and high-contrast light sheet fluorescence microscopic detection.
Collapse
|
3
|
Maharjan S, Ma C, Singh B, Kang H, Orive G, Yao J, Shrike Zhang Y. Advanced 3D imaging and organoid bioprinting for biomedical research and therapeutic applications. Adv Drug Deliv Rev 2024; 208:115237. [PMID: 38447931 PMCID: PMC11031334 DOI: 10.1016/j.addr.2024.115237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/15/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Organoid cultures offer a valuable platform for studying organ-level biology, allowing for a closer mimicry of human physiology compared to traditional two-dimensional cell culture systems or non-primate animal models. While many organoid cultures use cell aggregates or decellularized extracellular matrices as scaffolds, they often lack precise biochemical and biophysical microenvironments. In contrast, three-dimensional (3D) bioprinting allows precise placement of organoids or spheroids, providing enhanced spatial control and facilitating the direct fusion for the formation of large-scale functional tissues in vitro. In addition, 3D bioprinting enables fine tuning of biochemical and biophysical cues to support organoid development and maturation. With advances in the organoid technology and its potential applications across diverse research fields such as cell biology, developmental biology, disease pathology, precision medicine, drug toxicology, and tissue engineering, organoid imaging has become a crucial aspect of physiological and pathological studies. This review highlights the recent advancements in imaging technologies that have significantly contributed to organoid research. Additionally, we discuss various bioprinting techniques, emphasizing their applications in organoid bioprinting. Integrating 3D imaging tools into a bioprinting platform allows real-time visualization while facilitating quality control, optimization, and comprehensive bioprinting assessment. Similarly, combining imaging technologies with organoid bioprinting can provide valuable insights into tissue formation, maturation, functions, and therapeutic responses. This approach not only improves the reproducibility of physiologically relevant tissues but also enhances understanding of complex biological processes. Thus, careful selection of bioprinting modalities, coupled with appropriate imaging techniques, holds the potential to create a versatile platform capable of addressing existing challenges and harnessing opportunities in these rapidly evolving fields.
Collapse
Affiliation(s)
- Sushila Maharjan
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA
| | - Chenshuo Ma
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Bibhor Singh
- Winthrop L. Chenery Upper Elementary School, Belmont, MA 02478, USA
| | - Heemin Kang
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea; College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Gorka Orive
- NanoBioCel Research Group, School of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain; Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain; Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN). Vitoria-Gasteiz, Spain; University Institute for Regenerative Medicine and Oral Implantology - UIRMI (UPV/EHU-Fundación Eduardo Anitua), Vitoria, 01007, Spain; Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, Singapore 169856, Singapore
| | - Junjie Yao
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA.
| |
Collapse
|
4
|
Nguyen CD, Chen Y, Kaplan DL, Mallidi S. Multi-spectral photoacoustic imaging combined with acoustic radiation force impulse imaging for applications in tissue engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590806. [PMID: 38712117 PMCID: PMC11071356 DOI: 10.1101/2024.04.23.590806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Tissue engineering is a dynamic field focusing on the creation of advanced scaffolds for tissue and organ regeneration. These scaffolds are customized to their specific applications and are often designed to be complex, large structures to mimic tissues and organs. This study addresses the critical challenge of effectively characterizing these thick, optically opaque scaffolds that traditional imaging methods fail to fully image due to their optical limitations. We introduce a novel multi-modal imaging approach combining ultrasound, photoacoustic, and acoustic radiation force impulse imaging. This combination leverages its acoustic-based detection to overcome the limitations posed by optical imaging techniques. Ultrasound imaging is employed to monitor the scaffold structure, photoacoustic imaging is employed to monitor cell proliferation, and acoustic radiation force impulse imaging is employed to evaluate the homogeneity of scaffold stiffness. We applied this integrated imaging system to analyze melanoma cell growth within silk fibroin protein scaffolds with varying pore sizes and therefore stiffness over different cell incubation periods. Among various materials, silk fibroin was chosen for its unique combination of features including biocompatibility, tunable mechanical properties, and structural porosity which supports extensive cell proliferation. The results provide a detailed mesoscale view of the scaffolds' internal structure, including cell penetration depth and biomechanical properties. Our findings demonstrate that the developed multimodal imaging technique offers comprehensive insights into the physical and biological dynamics of tissue-engineered scaffolds. As the field of tissue engineering continues to advance, the importance of non-ionizing and non-invasive imaging systems becomes increasingly evident, and by facilitating a deeper understanding and better characterization of scaffold architectures, such imaging systems are pivotal in driving the success of future tissue-engineering solutions.
Collapse
|
5
|
Kairišs K, Sokolova N, Zilova L, Schlagheck C, Reinhardt R, Baumbach T, Faragó T, van de Kamp T, Wittbrodt J, Weinhardt V. Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach. Sci Rep 2024; 14:8543. [PMID: 38609416 PMCID: PMC11015006 DOI: 10.1038/s41598-024-58766-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The development of an organism is orchestrated by the spatial and temporal expression of genes. Accurate visualisation of gene expression patterns in the context of the surrounding tissues offers a glimpse into the mechanisms that drive morphogenesis. We developed correlative light-sheet fluorescence microscopy and X-ray computed tomography approach to map gene expression patterns to the whole organism`s 3D anatomy. We show that this multimodal approach is applicable to gene expression visualized by protein-specific antibodies and fluorescence RNA in situ hybridisation offering a detailed understanding of individual phenotypic variations in model organisms. Furthermore, the approach offers a unique possibility to identify tissues together with their 3D cellular and molecular composition in anatomically less-defined in vitro models, such as organoids. We anticipate that the visual and quantitative insights into the 3D distribution of gene expression within tissue architecture, by multimodal approach developed here, will be equally valuable for reference atlases of model organisms development, as well as for comprehensive screens, and morphogenesis studies of in vitro models.
Collapse
Affiliation(s)
- Kristaps Kairišs
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Lucie Zilova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
| | - Christina Schlagheck
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Robert Reinhardt
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tomáš Faragó
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Thomas van de Kamp
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | | | | |
Collapse
|
6
|
Pesce L, Ricci P, Sportelli G, Belcari N, Sancataldo G. Expansion and Light-Sheet Microscopy for Nanoscale 3D Imaging. SMALL METHODS 2024:e2301715. [PMID: 38461540 DOI: 10.1002/smtd.202301715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/10/2024] [Indexed: 03/12/2024]
Abstract
Expansion Microscopy (ExM) and Light-Sheet Fluorescence Microscopy (LSFM) are forefront imaging techniques that enable high-resolution visualization of biological specimens. ExM enhances nanoscale investigation using conventional fluorescence microscopes, while LSFM offers rapid, minimally invasive imaging over large volumes. This review explores the joint advancements of ExM and LSFM, focusing on the excellent performance of the integrated modality obtained from the combination of the two, which is refer to as ExLSFM. In doing so, the chemical processes required for ExM, the tailored optical setup of LSFM for examining expanded samples, and the adjustments in sample preparation for accurate data collection are emphasized. It is delve into various specimen types studied using this integrated method and assess its potential for future applications. The goal of this literature review is to enrich the comprehension of ExM and LSFM, encouraging their wider use and ongoing development, looking forward to the upcoming challenges, and anticipating innovations in these imaging techniques.
Collapse
Affiliation(s)
- Luca Pesce
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Pietro Ricci
- Department of Applied Physics, University of Barcelona, C/Martí i Franquès, 1, Barcelona, 08028, Spain
| | - Giancarlo Sportelli
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Nicola Belcari
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Giuseppe Sancataldo
- Department of Physics - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, Palermo, 90128, Italy
| |
Collapse
|
7
|
Sarhadi TR, Panse JS, Nagotu S. Mind the gap: Methods to study membrane contact sites. Exp Cell Res 2023; 431:113756. [PMID: 37633408 DOI: 10.1016/j.yexcr.2023.113756] [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: 03/28/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/28/2023]
Abstract
Organelles are dynamic entities whose functions are essential for the optimum functioning of cells. It is now known that the juxtaposition of organellar membranes is essential for the exchange of metabolites and their communication. These functional apposition sites are termed membrane contact sites. Dynamic membrane contact sites between various sub-cellular structures such as mitochondria, endoplasmic reticulum, peroxisomes, Golgi apparatus, lysosomes, lipid droplets, plasma membrane, endosomes, etc. have been reported in various model systems. The burgeoning area of research on membrane contact sites has witnessed several manuscripts in recent years that identified the contact sites and components involved. Several methods have been developed to identify, measure and analyze the membrane contact sites. In this manuscript, we aim to discuss important methods developed to date that are used to study membrane contact sites.
Collapse
Affiliation(s)
- Tanveera Rounaque Sarhadi
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Janhavee Shirish Panse
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| |
Collapse
|
8
|
Way GP, Sailem H, Shave S, Kasprowicz R, Carragher NO. Evolution and impact of high content imaging. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:292-305. [PMID: 37666456 DOI: 10.1016/j.slasd.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/09/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
The field of high content imaging has steadily evolved and expanded substantially across many industry and academic research institutions since it was first described in the early 1990's. High content imaging refers to the automated acquisition and analysis of microscopic images from a variety of biological sample types. Integration of high content imaging microscopes with multiwell plate handling robotics enables high content imaging to be performed at scale and support medium- to high-throughput screening of pharmacological, genetic and diverse environmental perturbations upon complex biological systems ranging from 2D cell cultures to 3D tissue organoids to small model organisms. In this perspective article the authors provide a collective view on the following key discussion points relevant to the evolution of high content imaging: • Evolution and impact of high content imaging: An academic perspective • Evolution and impact of high content imaging: An industry perspective • Evolution of high content image analysis • Evolution of high content data analysis pipelines towards multiparametric and phenotypic profiling applications • The role of data integration and multiomics • The role and evolution of image data repositories and sharing standards • Future perspective of high content imaging hardware and software.
Collapse
Affiliation(s)
- Gregory P Way
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Heba Sailem
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
| | - Steven Shave
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Rd, Stevenage SG1 2NY, UK; Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, UK
| | - Richard Kasprowicz
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Rd, Stevenage SG1 2NY, UK
| | - Neil O Carragher
- Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, UK.
| |
Collapse
|
9
|
Teranikar T, Nguyen P, Lee J. Biomechanics of cardiac development in zebrafish model. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023. [DOI: 10.1016/j.cobme.2023.100459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
|
10
|
Mueller JPJ, Dobosz M, O’Brien N, Abdoush N, Giusti AM, Lechmann M, Osl F, Wolf AK, Arellano-Viera E, Shaikh H, Sauer M, Rosenwald A, Herting F, Umaña P, Colombetti S, Pöschinger T, Beilhack A. ROCKETS - a novel one-for-all toolbox for light sheet microscopy in drug discovery. Front Immunol 2023; 14:1034032. [PMID: 36845124 PMCID: PMC9945347 DOI: 10.3389/fimmu.2023.1034032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/06/2023] [Indexed: 02/10/2023] Open
Abstract
Advancing novel immunotherapy strategies requires refined tools in preclinical research to thoroughly assess drug targets, biodistribution, safety, and efficacy. Light sheet fluorescence microscopy (LSFM) offers unprecedented fast volumetric ex vivo imaging of large tissue samples in high resolution. Yet, to date laborious and unstandardized tissue processing procedures have limited throughput and broader applications in immunological research. Therefore, we developed a simple and harmonized protocol for processing, clearing and imaging of all mouse organs and even entire mouse bodies. Applying this Rapid Optical Clearing Kit for Enhanced Tissue Scanning (ROCKETS) in combination with LSFM allowed us to comprehensively study the in vivo biodistribution of an antibody targeting Epithelial Cell Adhesion Molecule (EpCAM) in 3D. Quantitative high-resolution scans of whole organs did not only reveal known EpCAM expression patterns but, importantly, uncovered several new EpCAM-binding sites. We identified gustatory papillae of the tongue, choroid plexi in the brain and duodenal papillae as previously unanticipated locations of high EpCAM expression. Subsequently, we confirmed high EpCAM expression also in human tongue and duodenal specimens. Choroid plexi and duodenal papillae may be considered as particularly sensitive sites due to their importance for liquor production or as critical junctions draining bile and digestive pancreatic enzymes into the small bowel, respectively. These newly gained insights appear highly relevant for clinical translation of EpCAM-addressing immunotherapies. Thus, ROCKETS in combination with LSFM may help to set new standards for preclinical evaluation of immunotherapeutic strategies. In conclusion, we propose ROCKETS as an ideal platform for a broader application of LSFM in immunological research optimally suited for quantitative co-localization studies of immunotherapeutic drugs and defined cell populations in the microanatomical context of organs or even whole mice.
Collapse
Affiliation(s)
- Joerg P. J. Mueller
- Interdisciplinary Center for Clinical Research Laboratory (IZKF) Würzburg, Department of Internal Medicine II, Center for Experimental Molecular Medicine, Würzburg University Hospital, Würzburg, Germany
- Pharmaceutical Research and Early Development, Roche Diagnostics GmbH, Penzberg, Germany
| | - Michael Dobosz
- Pharmaceutical Research and Early Development, Roche Diagnostics GmbH, Penzberg, Germany
| | - Nils O’Brien
- Pharmaceutical Research and Early Development, Roche Diagnostics GmbH, Penzberg, Germany
| | - Nassri Abdoush
- Pharmaceutical Research and Early Development, Roche Diagnostics GmbH, Penzberg, Germany
| | - Anna Maria Giusti
- Roche Pharmaceutical Research and Early Development, Roche Glycart AG, Schlieren, Switzerland
| | - Martin Lechmann
- Pharmaceutical Research and Early Development, Roche Diagnostics GmbH, Penzberg, Germany
| | - Franz Osl
- Pharmaceutical Research and Early Development, Roche Diagnostics GmbH, Penzberg, Germany
| | - Ann-Katrin Wolf
- Interdisciplinary Center for Clinical Research Laboratory (IZKF) Würzburg, Department of Internal Medicine II, Center for Experimental Molecular Medicine, Würzburg University Hospital, Würzburg, Germany
- Pharmaceutical Research and Early Development, Roche Diagnostics GmbH, Penzberg, Germany
| | - Estibaliz Arellano-Viera
- Interdisciplinary Center for Clinical Research Laboratory (IZKF) Würzburg, Department of Internal Medicine II, Center for Experimental Molecular Medicine, Würzburg University Hospital, Würzburg, Germany
| | - Haroon Shaikh
- Interdisciplinary Center for Clinical Research Laboratory (IZKF) Würzburg, Department of Internal Medicine II, Center for Experimental Molecular Medicine, Würzburg University Hospital, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Frank Herting
- Pharmaceutical Research and Early Development, Roche Diagnostics GmbH, Penzberg, Germany
| | - Pablo Umaña
- Roche Pharmaceutical Research and Early Development, Roche Glycart AG, Schlieren, Switzerland
| | - Sara Colombetti
- Roche Pharmaceutical Research and Early Development, Roche Glycart AG, Schlieren, Switzerland
| | - Thomas Pöschinger
- Pharmaceutical Research and Early Development, Roche Diagnostics GmbH, Penzberg, Germany
| | - Andreas Beilhack
- Interdisciplinary Center for Clinical Research Laboratory (IZKF) Würzburg, Department of Internal Medicine II, Center for Experimental Molecular Medicine, Würzburg University Hospital, Würzburg, Germany
| |
Collapse
|
11
|
Cao Y, Lee S, Kim K, Kang SH. Minimizing the Optical Illusion of Nanoparticles in Single Cells Using Four-Dimensional Cuboid Multiangle Illumination-Based Light-Sheet Super-Resolution Imaging. Anal Chem 2022; 94:17877-17884. [PMID: 36509731 DOI: 10.1021/acs.analchem.2c03729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although light-sheet-based super-resolution microscopy is an excellent detection technique for biological samples because of minimal photodamage, uneven light paths due to solid-angle illumination limits it, resulting in an optical illusion. Furthermore, the optical illusion limits the observations of individual molecules in diffraction. In this study, a four-dimensional cuboid multiangle illumination-based light-sheet super-resolution (4D CMLS) imaging system was developed to minimize optical illusions in cells. The lab-built 4D CMLS imaging system was integrated with total internal reflection fluorescence and a differential interference contrast microscope. A specially designed rotatable cuboid prism simply overcame the optical illusion by rotating a specimen on the prism to change the direction of light coming from an illumination lens. 4D CMLS reconstructed images of nanoparticles of different sizes were acquired in multi-illumination angles of 0°, 90°, 180°, and 270°. Additionally, a 4D multiangle illumination-based algorithm was created to select the optimal illumination angle by combining three-dimensional super-resolution imaging with multiangle observation, even in the presence of obstacles. The 4D CMLS imaging method demonstrates the in-depth 4D observation of samples at an optimum angle that can be used in various applications, such as single-molecule and subcellular organelle observations in single cells at subdiffraction limit resolutions that describe the scenario of nature.
Collapse
Affiliation(s)
- Yingying Cao
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Kyungsoo Kim
- Department of Applied Mathematics, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Seong Ho Kang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea.,Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| |
Collapse
|
12
|
Lichtenegger A, Baumann B, Yasuno Y. Optical Coherence Tomography Is a Promising Tool for Zebrafish-Based Research-A Review. Bioengineering (Basel) 2022; 10:5. [PMID: 36671577 PMCID: PMC9854701 DOI: 10.3390/bioengineering10010005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
The zebrafish is an established vertebrae model in the field of biomedical research. With its small size, rapid maturation time and semi-transparency at early development stages, it has proven to be an important animal model, especially for high-throughput studies. Three-dimensional, high-resolution, non-destructive and label-free imaging techniques are perfectly suited to investigate these animals over various development stages. Optical coherence tomography (OCT) is an interferometric-based optical imaging technique that has revolutionized the diagnostic possibilities in the field of ophthalmology and has proven to be a powerful tool for many microscopic applications. Recently, OCT found its way into state-of-the-art zebrafish-based research. This review article gives an overview and a discussion of the relevant literature and an outlook for this emerging field.
Collapse
Affiliation(s)
- Antonia Lichtenegger
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria
- Computational Optics Group, University of Tsukuba, Tsukuba 305-8573, Japan
| | - Bernhard Baumann
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tsukuba 305-8573, Japan
| |
Collapse
|
13
|
Tang WC, Liu YT, Yeh CH, Lu CH, Tu CH, Lin YL, Lin YC, Hsu TL, Gao L, Chang SW, Chen P, Chen BC. Optogenetic manipulation of cell migration with high spatiotemporal resolution using lattice lightsheet microscopy. Commun Biol 2022; 5:879. [PMID: 36028551 PMCID: PMC9418249 DOI: 10.1038/s42003-022-03835-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/09/2022] [Indexed: 12/02/2022] Open
Abstract
Lattice lightsheet microscopy (LLSM) featuring three-dimensional recording is improved to manipulate cellular behavior with subcellular resolution through optogenetic activation (optoLLSM). A position-controllable Bessel beam as a stimulation source is integrated into the LLSM to achieve spatiotemporal photoactivation by changing the spatial light modulator (SLM) patterns. Unlike the point-scanning in a confocal microscope, the lattice beams are capable of wide-field optical sectioning for optogenetic activation along the Bessel beam path.We show that the energy power required for optogenetic activations is lower than 1 nW (or 24 mWcm-2) for time-lapses of CRY2olig clustering proteins, and membrane ruffling can be induced at different locations within a cell with subcellular resolution through light-triggered recruitment of phosphoinositide 3-kinase. Moreover, with the epidermal growth factor receptor (EGFR) fused with CRY2olig, we are able to demonstrate guided cell migration using optogenetic stimulation for up to 6 h, where 463 imaging volumes are collected, without noticeable cellular damages. Using a Bessel beam as a simulation source allows the use of lattice lightsheet microscopy for spatiotemporal control of photoactivation, illustrated by the control of cellular migration behavior.
Collapse
Affiliation(s)
- Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yen-Ting Liu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Han Yeh
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Chiao-Hui Tu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.,Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Tsui-Ling Hsu
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Liang Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
| | - Shu-Wei Chang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Physics, Academia Sinica, Taipei, 11529, Taiwan.
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.
| |
Collapse
|
14
|
Cai Y, Chen Y, Xia Y, Zheng S, Liu Z, Shi K. Single-Lens Light-Sheet Fluorescence Microscopy Based on Micro-Mirror Array. LASER & PHOTONICS REVIEWS 2022; 16:2100026. [PMID: 36389089 PMCID: PMC9648671 DOI: 10.1002/lpor.202100026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Conventional light sheet fluorescence microscopy (LSFM) utilizes two perpendicularly arranged objective lenses for optical excitation and detection, respectively. Such a configuration often limits the use of high-numerical-aperture (NA) objectives or requires specially designed long-working-distance objectives. Here, a LSFM based on a micro-mirror array (MMA) to enable light sheet imaging with a single objective lens is reported. The planar fluorescent emission excited by the light sheet illumination is collected by the same objective, relayed onto an MMA and detected by a side-view camera. The proposed scheme makes LSFM compatible to single objective imaging system and shows promising candidacy for high spatiotemporal imaging.
Collapse
Affiliation(s)
- Yanhui Cai
- State Key Laboratory for Mesoscopic Physics, Department of Physics, Peking University, Beijing 100871, P. R. China; Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, P. R. China
| | - Yizhu Chen
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yiqiu Xia
- Department of Biomedical Engineering, Penn State Material Research Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Siyang Zheng
- Biomedical Engineering and Electrical & Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Zhiwen Liu
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kebin Shi
- State Key Laboratory for Mesoscopic Physics, Department of Physics, Peking University, Beijing 100871, P. R. China; Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, P. R. China; Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, P. R. China
| |
Collapse
|
15
|
Nackenhorst MC, Kasiri M, Gollackner B, Regele H. Ex vivo fluorescence confocal microscopy: chances and changes in the analysis of breast tissue. Diagn Pathol 2022; 17:55. [PMID: 35765032 PMCID: PMC9238046 DOI: 10.1186/s13000-022-01240-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background Rapid histologic diagnosis of frozen sections is essential for a variety of surgical procedures. Frozen sections however, require specialized lab equipment, are prone to freezing artifacts and are not applicable to all types of tissue. Adipose tissue is especially difficult to process in frozen sections. Although these limitations are well known, no alternative method for microscopic tissue analysis that might replace frozen sections could be established. Our objective was to evaluate whether tissue imaging based on ex vivo fluorescent confocal microscopy (FCM) is applicable for rapid microscopic assessment of breast tumors specimens with abundant adipose tissue. Methods We evaluated 17 tissue samples from mastectomy specimens, rich in adipose tissue, submitted to the department of pathology at the Medical University of Vienna. We conducted our study on the FCM VivaScope® 2500M-G4 (Mavig GmbH, Munich, Germany; Caliber I.D.; Rochester NY, USA). Results When comparing FCM to frozen sections, we found a very similar overall processing time for FCM images and frozen sections respectively. Image quality was mostly superior to frozen sections (especially for adipose tissue and nuclear detail) but inferior to H&E stained FFPE sections. Limitations of the technology were uneven coloring, invisibility of ink applied for marking tissue margins and distortion artifacts if too much pressure is applied to the tissue. Conclusion FCM has the potential to expand the application and usefulness of rapid tissue analysis as speed is comparable and quality exceeds that of frozen sections especially in tissues rich in adipose cells such as breast specimen.
Collapse
Affiliation(s)
| | - Mohammad Kasiri
- Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Bernd Gollackner
- Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Heinz Regele
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
16
|
Wanderi K, Cui Z. Organic fluorescent nanoprobes with NIR-IIb characteristics for deep learning. EXPLORATION (BEIJING, CHINA) 2022; 2:20210097. [PMID: 37323884 PMCID: PMC10191020 DOI: 10.1002/exp.20210097] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/06/2022] [Indexed: 06/15/2023]
Abstract
Illumination of biological events with near-infrared II sub-channel (NIR-IIb, 1500-1700 nm) enhances the transparency of biological tissues, which is very attractive for deep imaging. Due to the long-wavelength, which reduces optical damage, suppresses autofluorescence, and obviates light scattering, NIR-IIb nanoprobes afford deep tissue penetration with unprecedented spatiotemporal resolution. Hence, NIR-IIb imaging facilitates deep learning and decipherment of biological proceedings in living organisms with astounding high clarity. In comparison to its predecessors in the visible-near-infrared spectrum, imaging in the NIR-IIb has shown great potential for tissue imaging and extrapolating imaging applications for clinical studies. However, the use of organic fluorescent nanoprobes (OFNPs) in the NIR-IIb region is still rare since it is in its early stages. Thus, herein we aim to survey the recent development of different organic fluorescent nanomaterials with NIR-IIb characteristics, their unique photophysical properties, and their utilization in deep imaging in animal models. Further, practical researches on organic fluorescent nanoprobes with NIR-IIb emission and their transition to clinical applications are highlighted.
Collapse
Affiliation(s)
- Kevin Wanderi
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
- Department of Analytical Microbiology and NanobiologyUniversity of Chinese Academy of SciencesBeijingChina
| | - Zongqiang Cui
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| |
Collapse
|
17
|
Bennett HC, Kim Y. Advances in studying whole mouse brain vasculature using high-resolution 3D light microscopy imaging. NEUROPHOTONICS 2022; 9:021902. [PMID: 35402638 PMCID: PMC8983067 DOI: 10.1117/1.nph.9.2.021902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Significance: The cerebrovasculature has become increasingly recognized as a major player in overall brain health and many brain disorders. Although there have been several landmark studies to understand details of these crucially important structures in an anatomically defined area, brain-wide examination of the whole cerebrovasculature, including microvessels, has been challenging. However, emerging techniques, including tissue processing and three-dimensional (3D) microscopy imaging, enable neuroscientists to examine the total vasculature in the entire mouse brain. Aim: Here, we aim to highlight advances in these high-resolution 3D mapping methods including block-face imaging and light sheet fluorescent microscopy. Approach: We summarize latest mapping tools to understand detailed anatomical arrangement of the cerebrovascular network and the organizing principles of the neurovascular unit (NVU) as a whole. Results: We discuss biological insights gained from studies using these imaging methods and how these tools can be used to advance our understanding of the cerebrovascular network and related cell types in the entire brain. Conclusions: This review article will help to understand recent advance in high-resolution NVU mapping in mice and provide perspective on future studies.
Collapse
Affiliation(s)
- Hannah C. Bennett
- The Pennsylvania State University, Department of Neural and Behavioral Sciences, Hershey, Pennsylvania, United States
| | - Yongsoo Kim
- The Pennsylvania State University, Department of Neural and Behavioral Sciences, Hershey, Pennsylvania, United States
| |
Collapse
|
18
|
Fei K, Zhang J, Yuan J, Xiao P. Present Application and Perspectives of Organoid Imaging Technology. Bioengineering (Basel) 2022; 9:bioengineering9030121. [PMID: 35324810 PMCID: PMC8945799 DOI: 10.3390/bioengineering9030121] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/23/2022] [Accepted: 03/13/2022] [Indexed: 11/18/2022] Open
Abstract
An organoid is a miniaturized and simplified in vitro model with a similar structure and function to a real organ. In recent years, the use of organoids has increased explosively in the field of growth and development, disease simulation, drug screening, cell therapy, etc. In order to obtain necessary information, such as morphological structure, cell function and dynamic signals, it is necessary and important to directly monitor the culture process of organoids. Among different detection technologies, imaging technology is a simple and convenient choice and can realize direct observation and quantitative research. In this review, the principle, advantages and disadvantages of imaging technologies that have been applied in organoids research are introduced. We also offer an overview of prospective technologies for organoid imaging. This review aims to help biologists find appropriate imaging techniques for different areas of organoid research, and also contribute to the development of organoid imaging systems.
Collapse
|
19
|
Ovečka M, Sojka J, Tichá M, Komis G, Basheer J, Marchetti C, Šamajová O, Kuběnová L, Šamaj J. Imaging plant cells and organs with light-sheet and super-resolution microscopy. PLANT PHYSIOLOGY 2022; 188:683-702. [PMID: 35235660 PMCID: PMC8825356 DOI: 10.1093/plphys/kiab349] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/12/2021] [Indexed: 05/05/2023]
Abstract
The documentation of plant growth and development requires integrative and scalable approaches to investigate and spatiotemporally resolve various dynamic processes at different levels of plant body organization. The present update deals with vigorous developments in mesoscopy, microscopy and nanoscopy methods that have been translated to imaging of plant subcellular compartments, cells, tissues and organs over the past 3 years with the aim to report recent applications and reasonable expectations from current light-sheet fluorescence microscopy (LSFM) and super-resolution microscopy (SRM) modalities. Moreover, the shortcomings and limitations of existing LSFM and SRM are discussed, particularly for their ability to accommodate plant samples and regarding their documentation potential considering spherical aberrations or temporal restrictions prohibiting the dynamic recording of fast cellular processes at the three dimensions. For a more comprehensive description, advances in living or fixed sample preparation methods are also included, supported by an overview of developments in labeling strategies successfully applied in plants. These strategies are practically documented by current applications employing model plant Arabidopsis thaliana (L.) Heynh., but also robust crop species such as Medicago sativa L. and Hordeum vulgare L. Over the past few years, the trend towards designing of integrative microscopic modalities has become apparent and it is expected that in the near future LSFM and SRM will be bridged to achieve broader multiscale plant imaging with a single platform.
Collapse
Affiliation(s)
- Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jiří Sojka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Michaela Tichá
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - George Komis
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jasim Basheer
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Cintia Marchetti
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Lenka Kuběnová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
- Author for communication:
| |
Collapse
|
20
|
Becker K, Saghafi S, Pende M, Hahn C, Dodt HU. Visualizing minute details in light-sheet and confocal microscopy data by combining 3D rolling ball filtering and deconvolution. JOURNAL OF BIOPHOTONICS 2022; 15:e202100290. [PMID: 34726837 DOI: 10.1002/jbio.202100290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
We developed an open-source deconvolution software that stunningly increases the visibility of minute details, as for example, neurons or nerve fibers in light-sheet microscopy or confocal microscopy data by combining rolling ball background subtraction in three directions with deconvolution using a synthetic or measured point spread function. Via automatic block-wise processing image stacks of virtually unlimited size can be deconvolved even on small computers with 8 or 16 GB RAM. By parallelization and optional GPU-acceleration, the software works with high speed: On a PC equipped with a state-of-the-art NVidia graphic board a three dimensional (3D)-stack of about 1 billion voxels can be deconvolved within 5 to 10 minutes. The implemented variation of the Richardson-Lucy deconvolution algorithm preserves the photogrammetry of the image data by using flux-preserving regularization, an approach that to our knowledge has not been applied for deconvolving microscopy data before.
Collapse
Affiliation(s)
- Klaus Becker
- Department of Bioelectronics, FKE, Vienna University of Technology, Vienna, Austria
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Saiedeh Saghafi
- Department of Bioelectronics, FKE, Vienna University of Technology, Vienna, Austria
| | - Marko Pende
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Mount Desert Island Biological Laboratory (MDIBL), Bar Harbor, Maine, USA
| | - Christian Hahn
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Hans Ulrich Dodt
- Department of Bioelectronics, FKE, Vienna University of Technology, Vienna, Austria
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
21
|
Jannasch A, Szilagyi SA, Burmeister M, Davis QT, Hermsdorf GL, De S, Schäffer E. Fast 3D imaging of giant unilamellar vesicles using reflected light-sheet microscopy with single molecule sensitivity. J Microsc 2021; 285:40-51. [PMID: 34786705 DOI: 10.1111/jmi.13070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/13/2021] [Indexed: 11/29/2022]
Abstract
Observation of highly dynamic processes inside living cells at the single molecule level is key for a better understanding of biological systems. However, imaging of single molecules in living cells is usually limited by the spatial and temporal resolution, photobleaching and the signal-to-background ratio. To overcome these limitations, light-sheet microscopes with thin selective plane illumination, for example, in a reflected geometry with a high numerical aperture imaging objective, have been developed. Here, we developed a reflected light-sheet microscope with active optics for fast, high contrast, two-colour acquisition of z -stacks. We demonstrate fast volume scanning by imaging a two-colour giant unilamellar vesicle (GUV) hemisphere. In addition, the high contrast enabled the imaging and tracking of single lipids in the GUV cap. The enhanced reflected scanning light-sheet microscope enables fast 3D scanning of artificial membrane systems and potentially live cells with single-molecule sensitivity and thereby could provide quantitative and molecular insight into the operation of cells.
Collapse
Affiliation(s)
- Anita Jannasch
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
| | - Sven A Szilagyi
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany.,Max Planck Institute for Solid State Physics, Heisenbergstrasse 1, Stuttgart, Germany
| | - Moritz Burmeister
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
| | - Q Tyrell Davis
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany.,School of Life Sciences, University of Dundee, Dow Street, Dundee, Scotland, UK
| | - Gero L Hermsdorf
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
| | - Suman De
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany.,Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Broomhall, Sheffield, UK
| | - Erik Schäffer
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
| |
Collapse
|
22
|
Live-cell visualization of cytochrome c: a tool to explore apoptosis. Biochem Soc Trans 2021; 49:2903-2915. [PMID: 34747968 DOI: 10.1042/bst20211028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023]
Abstract
Apoptosis dysfunction is associated with several malignancies, including cancer and autoimmune diseases. Apoptosis restoration could be an attractive therapeutic approach to those diseases. Mitochondrial outer membrane permeabilization is regarded as the point of no return in the 'classical' apoptosis triggering pathway. Cytoplasmic release of cytochrome c (cyt c), a mitochondrial electron transporter, is a prominent indicator of such critical step. Therefore, visualizing cyt c efflux in living cells is a convenient approach to address apoptosis triggering and monitor performance of apoptosis restoration strategies. Recent years have been prolific in the development of biosensors to visualize cyt c mitochondrial efflux in living cells, by fluorescence microscopy. These biosensors specifically detect endogenous, untagged cyt c, while showing efficient cellular uptake and reduced cell toxicity. A common aspect is their fluorescence quenching in the absence or presence of bound cyt c, resulting in two main biosensor types: 'turn ON' and 'turn OFF'. In some of these systems, fluorescence intensity of fluorophore-bound aptamers is enhanced upon cyt c binding. In others, cyt c binding to quantum dots quenches their fluorescence. In the present minireview, I describe these biosensors and briefly introduce some hypotheses that could be addressed using these novel tools.
Collapse
|
23
|
Valli J, Sanderson J. Super-Resolution Fluorescence Microscopy Methods for Assessing Mouse Biology. Curr Protoc 2021; 1:e224. [PMID: 34436832 DOI: 10.1002/cpz1.224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Super-resolution (diffraction unlimited) microscopy was developed 15 years ago; the developers were awarded the Nobel Prize in Chemistry in recognition of their work in 2014. Super-resolution microscopy is increasingly being applied to diverse scientific fields, from single molecules to cell organelles, viruses, bacteria, plants, and animals, especially the mammalian model organism Mus musculus. In this review, we explain how super-resolution microscopy, along with fluorescence microscopy from which it grew, has aided the renaissance of the light microscope. We cover experiment planning and specimen preparation and explain structured illumination microscopy, super-resolution radial fluctuations, stimulated emission depletion microscopy, single-molecule localization microscopy, and super-resolution imaging by pixel reassignment. The final section of this review discusses the strengths and weaknesses of each super-resolution technique and how to choose the best approach for your research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.
Collapse
Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| |
Collapse
|
24
|
R Moghadam M, Chen YPP. Tracking leukocytes in intravital time lapse images using 3D cell association learning network. Artif Intell Med 2021; 118:102129. [PMID: 34412846 DOI: 10.1016/j.artmed.2021.102129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/30/2021] [Accepted: 06/22/2021] [Indexed: 11/28/2022]
Abstract
Leukocytes are key cellular elements of the innate immune system in all vertebrates, which play a crucial role in defending organisms against invading pathogens. Tracking these highly migratory and amorphous cells in in vivo models such as zebrafish embryos is a challenging task in cellular immunology. As temporal and special analysis of these imaging datasets by a human operator is quite laborious, developing an automated cell tracking method is highly in demand. Despite the remarkable advances in cell detection, this field still lacks powerful algorithms to accurately associate the detected cell across time frames. The cell association challenge is mostly related to the amorphous nature of cells, and their complicated motion profile through their migratory paths. To tackle the cell association challenge, we proposed a novel deep-learning-based object linkage method. For this aim, we trained the 3D cell association learning network (3D-CALN) with enough manually labelled paired 3D images of single fluorescent zebrafish's neutrophils from two consecutive frames. Our experiment results prove that deep learning is significantly applicable in cell linkage and particularly for tracking highly mobile and amorphous leukocytes. A comparison of our tracking accuracy with other available tracking algorithms shows that our approach performs well in relation to addressing cell tracking problems.
Collapse
Affiliation(s)
- Marzieh R Moghadam
- Department of Computer Science and Information Technology, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - Yi-Ping Phoebe Chen
- Department of Computer Science and Information Technology, La Trobe University, Melbourne, Victoria 3086, Australia.
| |
Collapse
|
25
|
Ricci P, Gavryusev V, Müllenbroich C, Turrini L, de Vito G, Silvestri L, Sancataldo G, Pavone FS. Removing striping artifacts in light-sheet fluorescence microscopy: a review. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 168:52-65. [PMID: 34274370 DOI: 10.1016/j.pbiomolbio.2021.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 11/24/2022]
Abstract
In recent years, light-sheet fluorescence microscopy (LSFM) has found a broad application for imaging of diverse biological samples, ranging from sub-cellular structures to whole animals, both in-vivo and ex-vivo, owing to its many advantages relative to point-scanning methods. By providing the selective illumination of sample single planes, LSFM achieves an intrinsic optical sectioning and direct 2D image acquisition, with low out-of-focus fluorescence background, sample photo-damage and photo-bleaching. On the other hand, such an illumination scheme is prone to light absorption or scattering effects, which lead to uneven illumination and striping artifacts in the images, oriented along the light sheet propagation direction. Several methods have been developed to address this issue, ranging from fully optical solutions to entirely digital post-processing approaches. In this work, we present them, outlining their advantages, performance and limitations.
Collapse
Affiliation(s)
- Pietro Ricci
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
| | | | - Lapo Turrini
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
| | - Giuseppe de Vito
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Neuroscience, Psychology, Drug Research and Child Health, Florence, 50139, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy; National Institute of Optics, National Research Council, Sesto Fiorentino, 50019, Italy
| | - Giuseppe Sancataldo
- University of Palermo, Department of Physics and Chemistry, Palermo, 90128, Italy.
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy; National Institute of Optics, National Research Council, Sesto Fiorentino, 50019, Italy.
| |
Collapse
|
26
|
Liu C, Bai C, Yu X, Yan S, Zhou Y, Li X, Min J, Yang Y, Dan D, Yao B. Extended field of view of light-sheet fluorescence microscopy by scanning multiple focus-shifted Gaussian beam arrays. OPTICS EXPRESS 2021; 29:6158-6168. [PMID: 33726142 DOI: 10.1364/oe.418707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) facilitates high temporal-spatial resolution, low photobleaching and phototoxicity for long-term volumetric imaging. However, when a high axial resolution or optical sectioning capability is required, the field of view (FOV) is limited. Here, we propose to generate a large FOV of light-sheet by scanning multiple focus-shifted Gaussian beam arrays (MGBA) while keeping the high axial resolution. The positions of the beam waists of the multiple Gaussian beam arrays are shifted in both axial and lateral directions in an optimized arranged pattern, and then scanned along the direction perpendicular to the propagation axis to form an extended FOV of light-sheet. Complementary beam subtraction method is also adopted to further improve axial resolution. Compared with the single Gaussian light-sheet method, the proposed method extends the FOV from 12 μm to 200 μm while sustaining the axial resolution of 0.73 μm. Both numerical simulation and experiment on samples are performed to verify the effectiveness of the method.
Collapse
|
27
|
Buglak NE, Lucitti J, Ariel P, Maiocchi S, Miller FJ, Bahnson ESM. Light sheet fluorescence microscopy as a new method for unbiased three-dimensional analysis of vascular injury. Cardiovasc Res 2021; 117:520-532. [PMID: 32053173 PMCID: PMC7820842 DOI: 10.1093/cvr/cvaa037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/02/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
AIMS Assessment of preclinical models of vascular disease is paramount in the successful translation of novel treatments. The results of these models have traditionally relied on two-dimensional (2D) histological methodologies. Light sheet fluorescence microscopy (LSFM) is an imaging platform that allows for three-dimensional (3D) visualization of whole organs and tissues. In this study, we describe an improved methodological approach utilizing LSFM for imaging of preclinical vascular injury models while minimizing analysis bias. METHODS AND RESULTS The rat carotid artery segmental pressure-controlled balloon injury and mouse carotid artery ligation injury were performed. Arteries were harvested and processed for LSFM imaging and 3D analysis, as well as for 2D area histological analysis. Artery processing for LSFM imaging did not induce vessel shrinkage or expansion and was reversible by rehydrating the artery, allowing for subsequent sectioning and histological staining a posteriori. By generating a volumetric visualization along the length of the arteries, LSFM imaging provided different analysis modalities including volumetric, area, and radial parameters. Thus, LSFM-imaged arteries provided more precise measurements compared to classic histological analysis. Furthermore, LSFM provided additional information as compared to 2D analysis in demonstrating remodelling of the arterial media in regions of hyperplasia and periadventitial neovascularization around the ligated mouse artery. CONCLUSION LSFM provides a novel and robust 3D imaging platform for visualizing and quantifying arterial injury in preclinical models. When compared with classic histology, LSFM outperformed traditional methods in precision and quantitative capabilities. LSFM allows for more comprehensive quantitation as compared to traditional histological methodologies, while minimizing user bias associated with area analysis of alternating, 2D histological artery cross-sections.
Collapse
Affiliation(s)
- Nicholas E Buglak
- Division of Vascular Surgery, Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Center for Nanotechnology in Drug Delivery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Toxicology & Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Pablo Ariel
- Microscopy Services Laboratory, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sophie Maiocchi
- Division of Vascular Surgery, Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Center for Nanotechnology in Drug Delivery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Francis J Miller
- Department of Medicine, Duke University, Durham, NC 27708, USA
- Department of Medicine, Veterans Administration Medical Center, Durham, NC 27705, USA
| | - Edward S M Bahnson
- Division of Vascular Surgery, Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Center for Nanotechnology in Drug Delivery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Toxicology & Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
28
|
Abstract
Microphysiological systems (MPS), often referred to as "organ-on-chips," are microfluidic-based in vitro models that aim to recapitulate the dynamic chemical and mechanical microenvironment of living organs. MPS promise to bridge the gap between in vitro and in vivo models and ultimately improve the translation from preclinical animal studies to clinical trials. However, despite the explosion of interest in this area in recent years, and the obvious rewards for such models that could improve R&D efficiency and reduce drug attrition in the clinic, the pharmaceutical industry has been slow to fully adopt this technology. The ability to extract robust, quantitative information from MPS at scale is a key requirement if these models are to impact drug discovery and the subsequent drug development process. Microscopy imaging remains a core technology that enables the capture of information at the single-cell level and with subcellular resolution. Furthermore, such imaging techniques can be automated, increasing throughput and enabling compound screening. In this review, we discuss a range of imaging techniques that have been applied to MPS of varying focus, such as organoids and organ-chip-type models. We outline the opportunities these technologies can bring in terms of understanding mechanistic biology, but also how they could be used in higher-throughput screens, widening the scope of their impact in drug discovery. We discuss the associated challenges of imaging these complex models and the steps required to enable full exploitation. Finally, we discuss the requirements for MPS, if they are to be applied at a scale necessary to support drug discovery projects.
Collapse
Affiliation(s)
- Samantha Peel
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Mark Jackman
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| |
Collapse
|
29
|
Wait EC, Reiche MA, Chew TL. Hypothesis-driven quantitative fluorescence microscopy - the importance of reverse-thinking in experimental design. J Cell Sci 2020; 133:133/21/jcs250027. [PMID: 33154172 DOI: 10.1242/jcs.250027] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
One of the challenges in modern fluorescence microscopy is to reconcile the conventional utilization of microscopes as exploratory instruments with their emerging and rapidly expanding role as a quantitative tools. The contribution of microscopy to observational biology will remain enormous owing to the improvements in acquisition speed, imaging depth, resolution and biocompatibility of modern imaging instruments. However, the use of fluorescence microscopy to facilitate the quantitative measurements necessary to challenge hypotheses is a relatively recent concept, made possible by advanced optics, functional imaging probes and rapidly increasing computational power. We argue here that to fully leverage the rapidly evolving application of microscopes in hypothesis-driven biology, we not only need to ensure that images are acquired quantitatively but must also re-evaluate how microscopy-based experiments are designed. In this Opinion, we present a reverse logic that guides the design of quantitative fluorescence microscopy experiments. This unique approach starts from identifying the results that would quantitatively inform the hypothesis and map the process backward to microscope selection. This ensures that the quantitative aspects of testing the hypothesis remain the central focus of the entire experimental design.
Collapse
Affiliation(s)
- Eric C Wait
- Advanced Imaging Center, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Michael A Reiche
- Advanced Imaging Center, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| |
Collapse
|
30
|
Sabdyusheva Litschauer I, Becker K, Saghafi S, Ballke S, Bollwein C, Foroughipour M, Gaugeler J, Foroughipour M, Schavelová V, László V, Döme B, Brostjan C, Weichert W, Dodt HU. 3D histopathology of human tumours by fast clearing and ultramicroscopy. Sci Rep 2020; 10:17619. [PMID: 33077794 PMCID: PMC7572501 DOI: 10.1038/s41598-020-71737-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/02/2020] [Indexed: 12/31/2022] Open
Abstract
Here, we describe a novel approach that allows pathologists to three-dimensionally analyse malignant tissues, including the tumour-host tissue interface. Our visualization technique utilizes a combination of ultrafast chemical tissue clearing and light-sheet microscopy to obtain virtual slices and 3D reconstructions of up to multiple centimetre sized tumour resectates. For the clearing of tumours we propose a preparation technique comprising three steps: (a) Fixation and enhancement of tissue autofluorescence with formalin/5-sulfosalicylic acid. (b) Ultrafast active chemical dehydration with 2,2-dimethoxypropane and (c) refractive index matching with dibenzyl ether at up to 56 °C. After clearing, the tumour resectates are imaged. The images are computationally post-processed for contrast enhancement and artefact removal and then 3D reconstructed. Importantly, the sequence a–c is fully reversible, allowing the morphological correlation of one and the same histological structures, once visualized with our novel technique and once visualized by standard H&E- and IHC-staining. After reverting the clearing procedure followed by standard H&E processing, the hallmarks of ductal carcinoma in situ (DCIS) found in the cleared samples could be successfully correlated with the corresponding structures present in H&E and IHC staining. Since the imaging of several thousands of optical sections is a fast process, it is possible to analyse a larger part of the tumour than by mechanical slicing. As this also adds further information about the 3D structure of malignancies, we expect that our technology will become a valuable addition for histological diagnosis in clinical pathology.
Collapse
Affiliation(s)
- Inna Sabdyusheva Litschauer
- Department of Bioelectronics, TU Wien, Vienna, Austria. .,Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| | - Klaus Becker
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Saiedeh Saghafi
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Simone Ballke
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Christine Bollwein
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Meraaj Foroughipour
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Julia Gaugeler
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Massih Foroughipour
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Viktória Schavelová
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Viktória László
- Department of Surgery, Anna Spiegel Center of Translational Research, Medical University of Vienna, Vienna, Austria
| | - Balazs Döme
- Department of Surgery, Anna Spiegel Center of Translational Research, Medical University of Vienna, Vienna, Austria
| | - Christine Brostjan
- Department of Surgery, Anna Spiegel Center of Translational Research, Medical University of Vienna, Vienna, Austria
| | - Wilko Weichert
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Hans-Ulrich Dodt
- Department of Bioelectronics, TU Wien, Vienna, Austria. .,Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
31
|
Heidari-Khoei H, Esfandiari F, Hajari MA, Ghorbaninejad Z, Piryaei A, Baharvand H. Organoid technology in female reproductive biomedicine. Reprod Biol Endocrinol 2020; 18:64. [PMID: 32552764 PMCID: PMC7301968 DOI: 10.1186/s12958-020-00621-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023] Open
Abstract
Recent developments in organoid technology are revolutionizing our knowledge about the biology, physiology, and function of various organs. Female reproductive biology and medicine also benefit from this technology. Organoids recapitulate features of different reproductive organs including the uterus, fallopian tubes, and ovaries, as well as trophoblasts. The genetic stability of organoids and long-lasting commitment to their tissue of origin during long-term culture makes them attractive substitutes for animal and in vitro models. Despite current limitations, organoids offer a promising platform to address fundamental questions regarding the reproductive system's physiology and pathology. They provide a human source to harness stem cells for regenerative medicine, heal damaged epithelia in specific diseases, and study biological processes in healthy and pathological conditions. The combination of male and female reproductive organoids with other technologies, such as microfluidics technology, would enable scientists to create a multi-organoid-on-a-chip platform for the next step to human-on-a-chip platforms for clinical applications, drug discovery, and toxicology studies. The present review discusses recent advances in producing organoid models of reproductive organs and highlights their applications, as well as technical challenges and future directions.
Collapse
Affiliation(s)
- Heidar Heidari-Khoei
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, P.O. Box: 16635-148, Tehran, 1665659911, Iran
| | - Fereshteh Esfandiari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, P.O. Box: 16635-148, Tehran, 1665659911, Iran
| | - Mohammad Amin Hajari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, P.O. Box: 16635-148, Tehran, 1665659911, Iran
| | - Zeynab Ghorbaninejad
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, P.O. Box: 16635-148, Tehran, 1665659911, Iran
| | - Abbas Piryaei
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, P.O. Box: 19395-4719, Tehran, Iran.
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, P.O. Box: 16635-148, Tehran, 1665659911, Iran.
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran.
| |
Collapse
|
32
|
Abstract
The light (or optical) microscope is the icon of science. The aphorism "seeing is believing" is often quoted in scientific papers involving microscopy. Unlike many scientific instruments, the light microscope will deliver an image however badly it is set up. Fluorescence microscopy is a widely used research tool across all disciplines of biological and biomedical science. Most universities and research institutions have microscopes, including confocal microscopes. This introductory paper in a series detailing advanced light microscopy techniques explains the foundations of both electron and light microscopy for biologists and life scientists working with the mouse. An explanation is given of how an image is formed. A description is given of how to set up a light microscope, whether it be a brightfield light microscope on the laboratory bench, a widefield fluorescence microscope, or a confocal microscope. These explanations are accompanied by operational protocols. A full explanation on how to set up and adjust a microscope according to the principles of Köhler illumination is given. The importance of Nyquist sampling is discussed. Guidelines are given on how to choose the best microscope to image the particular sample or slide preparation that you are working with. These are the basic principles of microscopy that a researcher must have an understanding of when operating core bioimaging facility instruments, in order to collect high-quality images. © 2020 The Authors. Basic Protocol 1: Setting up Köhler illumination for a brightfield microscope Basic Protocol 2: Aligning the fluorescence bulb and setting up Köhler illumination for a widefield fluorescence microscope Basic Protocol 3: Generic protocol for operating a confocal microscope.
Collapse
Affiliation(s)
- Jeremy Sanderson
- Bioimaging Facility Manager, MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| |
Collapse
|
33
|
Sato H, Das S, Singer RH, Vera M. Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression. Annu Rev Biochem 2020; 89:159-187. [PMID: 32176523 DOI: 10.1146/annurev-biochem-011520-104955] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review focuses on imaging DNA and single RNA molecules in living cells to define eukaryotic functional organization and dynamic processes. The latest advances in technologies to visualize individual DNA loci and RNAs in real time are discussed. Single-molecule fluorescence microscopy provides the spatial and temporal resolution to reveal mechanisms regulating fundamental cell functions. Novel insights into the regulation of nuclear architecture, transcription, posttranscriptional RNA processing, and RNA localization provided by multicolor fluorescence microscopy are reviewed. A perspective on the future use of live imaging technologies and overcoming their current limitations is provided.
Collapse
Affiliation(s)
- Hanae Sato
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , ,
| | - Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , ,
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , , .,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Maria Vera
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , , .,Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada;
| |
Collapse
|
34
|
Becker K, Saghafi S, Pende M, Sabdyusheva-Litschauer I, Hahn CM, Foroughipour M, Jährling N, Dodt HU. Deconvolution of light sheet microscopy recordings. Sci Rep 2019; 9:17625. [PMID: 31772375 PMCID: PMC6879637 DOI: 10.1038/s41598-019-53875-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/04/2019] [Indexed: 02/01/2023] Open
Abstract
We developed a deconvolution software for light sheet microscopy that uses a theoretical point spread function, which we derived from a model of image formation in a light sheet microscope. We show that this approach provides excellent blur reduction and enhancement of fine image details for image stacks recorded with low magnification objectives of relatively high NA and high field numbers as e.g. 2x NA 0.14 FN 22, or 4x NA 0.28 FN 22. For these objectives, which are widely used in light sheet microscopy, sufficiently resolved point spread functions that are suitable for deconvolution are difficult to measure and the results obtained by common deconvolution software developed for confocal microscopy are usually poor. We demonstrate that the deconvolutions computed using our point spread function model are equivalent to those obtained using a measured point spread function for a 10x objective with NA 0.3 and for a 20x objective with NA 0.45.
Collapse
Affiliation(s)
- Klaus Becker
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria.
- Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| | | | - Marko Pende
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Inna Sabdyusheva-Litschauer
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Christian M Hahn
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Massih Foroughipour
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Nina Jährling
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Hans-Ulrich Dodt
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
35
|
Chen CY, Liu YT, Lu CH, Lee PY, Tsai YC, Wu JS, Chen P, Chen BC. The Applications of Lattice Light-sheet Microscopy for Functional Volumetric Imaging of Hippocampal Neurons in a Three-Dimensional Culture System. MICROMACHINES 2019; 10:E599. [PMID: 31514427 PMCID: PMC6780203 DOI: 10.3390/mi10090599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/07/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022]
Abstract
The characterization of individual cells in three-dimensions (3D) with very high spatiotemporal resolution is crucial for the development of organs-on-chips, in which 3D cell cultures are integrated with microfluidic systems. In this study, we report the applications of lattice light-sheet microscopy (LLSM) for monitoring neuronal activity in three-dimensional cell culture. We first established a 3D environment for culturing primary hippocampal neurons by applying a scaffold-based 3D tissue engineering technique. Fully differentiated and mature hippocampal neurons were observed in our system. With LLSM, we were able to monitor the behavior of individual cells in a 3D cell culture, which was very difficult under a conventional microscope due to strong light scattering from thick samples. We demonstrated that our system could study the membrane voltage and intracellular calcium dynamics at subcellular resolution in 3D under both chemical and electrical stimulation. From the volumetric images, it was found that the voltage indicators mainly resided in the cytosol instead of the membrane, which cannot be distinguished using conventional microscopy. Neuronal volumetric images were sheet scanned along the axial direction and recorded at a laser exposure of 6 ms, which covered an area up to 4800 μm2, with an image pixel size of 0.102 μm. When we analyzed the time-lapse volumetric images, we could quantify the voltage responses in different neurites in 3D extensions.
Collapse
Affiliation(s)
- Chin-Yi Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Yen-Ting Liu
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Po-Yi Lee
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Yun-Chi Tsai
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Jyun-Sian Wu
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan.
| |
Collapse
|
36
|
Next-generation imaging of the skeletal system and its blood supply. Nat Rev Rheumatol 2019; 15:533-549. [PMID: 31395974 DOI: 10.1038/s41584-019-0274-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 12/16/2022]
Abstract
Bone is organized in a hierarchical 3D architecture. Traditionally, analysis of the skeletal system was based on bone mass assessment by radiographic methods or on the examination of bone structure by 2D histological sections. Advanced imaging technologies and big data analysis now enable the unprecedented examination of bone and provide new insights into its 3D macrostructure and microstructure. These technologies comprise ex vivo and in vivo methods including high-resolution computed tomography (CT), synchrotron-based imaging, X-ray microscopy, ultra-high-field magnetic resonance imaging (MRI), light-sheet fluorescence microscopy, confocal and intravital two-photon imaging. In concert, these techniques have been used to detect and quantify a novel vascular system of trans-cortical vessels in bone. Furthermore, structures such as the lacunar network, which harbours and connects osteocytes, become accessible for 3D imaging and quantification using these methods. Next-generation imaging of the skeletal system and its blood supply are anticipated to contribute to an entirely new understanding of bone tissue composition and function, from macroscale to nanoscale, in health and disease. These insights could provide the basis for early detection and precision-type intervention of bone disorders in the future.
Collapse
|
37
|
Kameneva P, Adameyko I. Recent advances in our understanding of central and peripheral nervous system progenitors. Curr Opin Cell Biol 2019; 61:24-30. [PMID: 31369951 DOI: 10.1016/j.ceb.2019.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/25/2019] [Accepted: 07/02/2019] [Indexed: 10/26/2022]
Abstract
Several decades of intense research provided us with a grand framework describing the emergence of neurons in central (CNS) and peripheral (PNS) nervous systems. However, the specifics of molecular events and lineage control leading to a plethora of neuronal subtypes stayed largely unclear. Today, the advances in single cell omics, sample clearing and 3D-microscopy techniques, brain organoids, and synaptic connectivity tracing enabled systematic and unbiased understanding of neuronal diversity, development, circuitry and cell identity control. Novel technological advancements stimulated the transition from conceptual scheme of neuronal differentiation into precise maps of molecular events leading to the diversity of specific neuronal subtypes in relation to their locations and microenvironment. These high-resolution data opened a set of new questions including how transcriptional and epigenetics states control the proportionality of neuronal subpopulations or what are the evolutionary mechanisms of origin of different neuronal subtypes. In this review, we outline the most recent advancements in our understanding of how the neuronal diversity is generated in CNS and PNS and briefly address the challenges and questions arising in the field of neurogenesis.
Collapse
Affiliation(s)
- Polina Kameneva
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Molecular Neurosciences, Center for Brain Research, Medical University Vienna, 1090 Vienna, Austria.
| |
Collapse
|
38
|
Charbonneau AM, Al-Samadi A, Salo T, Tran SD. 3D Culture Histology Cryosectioned Well Insert Technology Preserves the Structural Relationship between Cells and Biomaterials for Time-Lapse Analysis of 3D Cultures. Biotechnol J 2019; 14:e1900105. [PMID: 31294920 DOI: 10.1002/biot.201900105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/18/2019] [Indexed: 01/07/2023]
Abstract
When performing histology of softer biomaterials, aspiration disrupts the cellular and molecular location information. This study aims to develop a cryosectionable well insert able to preserve the biomaterial and cell's original 3D conformation from the well to histology analysis. The well insert is composed of a paraffin-coated gelatine pill. Within the coated capsule, the human epithelial cell line (NS-SV-AC) is cultured in Matrigel, GrowDex, Myogel, Myogel + GrowDex, or cell culture media for 14 days. At 0 and 14 days, the samples are frozen in liquid nitrogen and cryotome is used to create sections. The slides are stained by Sirius Red and immunohistochemistry using antibodies human collagens I-V and human Ki-67. Sirius Red shows pink shades of biomaterials and the best cellular vertical distribution throughout the sagittal section of the well is achieved with Matrigel, GrowDex, and Myogel + GrowDex; in Myogel and media, the cells sink. For collagen protein expression, only Matrigel induces a notable difference while in the other materials, collagen staining is weak or difficult to distinguish from endogenous collagens. Ki-67 expression is maintained over time. The 3D-cryo well insert provides a new time-lapse histology perspective of analysis for liquid or gel cultures that maintains cells and macromolecules in their unaltered in-well configuration.
Collapse
Affiliation(s)
- André M Charbonneau
- Faculty of Dentistry, McGill University, 3640 University Street, H3A 0C7, Montréal, Canada
| | - Ahmed Al-Samadi
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, 00014, Finland
| | - Tuula Salo
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, 00014, Finland
| | - Simon D Tran
- Faculty of Dentistry, McGill University, 3640 University Street, H3A 0C7, Montréal, Canada
| |
Collapse
|
39
|
Pratiwi FW, Kuo CW, Chen BC, Chen P. Recent advances in the use of fluorescent nanoparticles for bioimaging. Nanomedicine (Lond) 2019; 14:1759-1769. [DOI: 10.2217/nnm-2019-0105] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Rapid and recent progress in fluorescence microscopic techniques has allowed for routine discovery and viewing of biological structures and processes in unprecedented spatiotemporal resolution. In these imaging techniques, fluorescent nanoparticles (NPs) play important roles in the improvement of reporting systems. A short overview of recently developed fluorescent NPs used for advanced in vivo imaging will be discussed in this mini-review. The discussion begins with the contribution of fluorescence imaging in exploring the fate of NPs in biological systems. NP applications for in vivo imaging, including cell labeling, multimodal imaging and theranostic agents, are then discussed. Finally, despite all of the advancements in bioimaging, some unsolved challenges will be briefly discussed concerning future research directions.
Collapse
Affiliation(s)
| | - Chiung Wen Kuo
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
40
|
Vaz R, Hofmeister W, Lindstrand A. Zebrafish Models of Neurodevelopmental Disorders: Limitations and Benefits of Current Tools and Techniques. Int J Mol Sci 2019; 20:ijms20061296. [PMID: 30875831 PMCID: PMC6471844 DOI: 10.3390/ijms20061296] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
For the past few years there has been an exponential increase in the use of animal models to confirm the pathogenicity of candidate disease-causing genetic variants found in patients. One such animal model is the zebrafish. Despite being a non-mammalian animal, the zebrafish model has proven its potential in recapitulating the phenotypes of many different human genetic disorders. This review will focus on recent advances in the modeling of neurodevelopmental disorders in zebrafish, covering aspects from early brain development to techniques used for modulating gene expression, as well as how to best characterize the resulting phenotypes. We also review other existing models of neurodevelopmental disorders, and the current efforts in developing and testing compounds with potential therapeutic value.
Collapse
Affiliation(s)
- Raquel Vaz
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.
| | - Wolfgang Hofmeister
- Laboratory of Molecular and Cellular Cardiology, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense, Denmark and the Novo Nordisk Foundation for Stem cell Biology (Danstem), University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine and Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, 171 76 Stockholm, Sweden.
| |
Collapse
|