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Windell DL, Mourabit S, Moger J, Owen SF, Winter MJ, Tyler CR. The influence of size and surface chemistry on the bioavailability, tissue distribution and toxicity of gold nanoparticles in zebrafish (Danio rerio). Ecotoxicol Environ Saf 2023; 260:115019. [PMID: 37269610 DOI: 10.1016/j.ecoenv.2023.115019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/05/2023] [Accepted: 05/14/2023] [Indexed: 06/05/2023]
Abstract
Gold nanoparticles (AuNPs) are widely used in biomedicine and their specific properties including, size, geometrics, and surface coating, will affect their fate and behaviour in biological systems. These properties are well studied for their intended biological targets, but there is a lack of understanding on the mechanisms by which AuNPs interact in non-target organisms when they enter the environment. We investigated the effects of size and surface chemistry of AuNPs on their bioavailability, tissue distribution and potential toxicity using zebrafish (Danio rerio) as an experimental model. Larval zebrafish were exposed to fluorescently tagged AuNPs of different sizes (10-100 nm) and surface modifications (TNFα, NHS/PAMAM and PEG), and uptake, tissue distribution and depuration rates were measured using selective-plane illumination microscopy (SPIM). The gut and pronephric tubules were found to contain detectable levels of AuNPs, and the concentration-dependent accumulation was related to the particle size. Surface addition of PEG and TNFα appeared to enhance particle accumulation in the pronephric tubules compared to uncoated particles. Depuration studies showed a gradual removal of particles from the gut and pronephric tubules, although fluorescence indicating the presence of the AuNPs remained in the pronephros 96 h after exposure. Toxicity assessment using two transgenic zebrafish reporter lines, however, revealed no AuNP-related renal injury or cellular oxidative stress. Collectively, our data show that AuNPs used in medical applications across the size range 40-80 nm, are bioavailable to larval zebrafish and some may persist in renal tissue, although their presence did not result in measurable toxicity with respect to pronephric organ function or cellular oxidative stress for short term exposures.
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Affiliation(s)
- Dylan L Windell
- Biosciences, Faculty of Health and Life Sciences, Exeter, Devon EX4 4QD, United Kingdom
| | - Sulayman Mourabit
- Biosciences, Faculty of Health and Life Sciences, Exeter, Devon EX4 4QD, United Kingdom
| | - Julian Moger
- Physics and Medical Imaging, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, Devon EX4 4QL, United Kingdom
| | - Stewart F Owen
- AstraZeneca, Global Compliance, Alderley Park, Macclesfield, Cheshire SK10 4TF, United Kingdom
| | - Matthew J Winter
- Biosciences, Faculty of Health and Life Sciences, Exeter, Devon EX4 4QD, United Kingdom
| | - Charles R Tyler
- Biosciences, Faculty of Health and Life Sciences, Exeter, Devon EX4 4QD, United Kingdom.
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Mitrakas AG, Tsolou A, Didaskalou S, Karkaletsou L, Efstathiou C, Eftalitsidis E, Marmanis K, Koffa M. Applications and Advances of Multicellular Tumor Spheroids: Challenges in Their Development and Analysis. Int J Mol Sci 2023; 24:ijms24086949. [PMID: 37108113 PMCID: PMC10138394 DOI: 10.3390/ijms24086949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Biomedical research requires both in vitro and in vivo studies in order to explore disease processes or drug interactions. Foundational investigations have been performed at the cellular level using two-dimensional cultures as the gold-standard method since the early 20th century. However, three-dimensional (3D) cultures have emerged as a new tool for tissue modeling over the last few years, bridging the gap between in vitro and animal model studies. Cancer has been a worldwide challenge for the biomedical community due to its high morbidity and mortality rates. Various methods have been developed to produce multicellular tumor spheroids (MCTSs), including scaffold-free and scaffold-based structures, which usually depend on the demands of the cells used and the related biological question. MCTSs are increasingly utilized in studies involving cancer cell metabolism and cell cycle defects. These studies produce massive amounts of data, which demand elaborate and complex tools for thorough analysis. In this review, we discuss the advantages and disadvantages of several up-to-date methods used to construct MCTSs. In addition, we also present advanced methods for analyzing MCTS features. As MCTSs more closely mimic the in vivo tumor environment, compared to 2D monolayers, they can evolve to be an appealing model for in vitro tumor biology studies.
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Affiliation(s)
- Achilleas G Mitrakas
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Avgi Tsolou
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Stylianos Didaskalou
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Lito Karkaletsou
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Christos Efstathiou
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Evgenios Eftalitsidis
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Konstantinos Marmanis
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Maria Koffa
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
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Steindel M, Orsine de Almeida I, Strawbridge S, Chernova V, Holcman D, Ponjavic A, Basu S. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy. Methods Mol Biol 2022; 2476:209-247. [PMID: 35635707 DOI: 10.1007/978-1-0716-2221-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single-molecule localization microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal "snapshots" of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination, 3D SMLM, and protein labeling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analyzing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely, or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Maike Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Stanley Strawbridge
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Valentyna Chernova
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Aleks Ponjavic
- School of Physics and Astronomy and School of Food Science and Nutrition, University of Leeds, Leeds, UK.
| | - Srinjan Basu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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Fredrickson SJ, Hoog TG, Udan RS. Visualizing Blood Vessel Development in Cultured Mouse Embryos Using Lightsheet Microscopy. Methods Mol Biol 2021; 2319:93-104. [PMID: 34331247 DOI: 10.1007/978-1-0716-1480-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Lightsheet microscopy is a form of fluorescence microscopy that can be used to visualize specimen with high resolution, a large depth-of-field, and minimal photodamage and photobleaching as compared to traditional confocal microscopy. As this technology becomes much more readily available, it will be useful in revealing new findings in the cardiovascular development field that may be hidden or difficult to image. In this manuscript, we describe an approach for mounting and culturing postimplantation mouse embryos to visualize blood vessel development with a lightsheet microscope.
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Gava F, Faria C, Gravelle P, Valero JG, Dobaño-López C, Morin R, Norlund M, Gomes A, Lagarde JM, Rossi C, Bordenave J, Pieruccioni L, Rouquette J, Matas-Céspedes A, Fournié JJ, Ysebaert L, Laurent C, Pérez-Galán P, Bezombes C. 3D Model Characterization by 2D and 3D Imaging in t(14;18)-Positive B-NHL: Perspectives for In Vitro Drug Screens in Follicular Lymphoma. Cancers (Basel) 2021; 13:1490. [PMID: 33804934 DOI: 10.3390/cancers13071490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Follicular lymphoma is an indolent B cell lymphoproliferative disorder of transformed follicular center B cells, which accounts for 20–30 percent of all non-Hodgkin lymphoma (NHL) cases. Although huge efforts have been made in the last 10 years, this pathology is still considered as incurable, leaving open the discovery and testing of new therapeutic targets requiring relevant preclinical models. Here, we report a realistic 3D model of t (14;18)-positive B-NHL cell culture (ultra-low attachment (ULA)-multicellular aggregates of lymphoma cells (MALC)), which monitored by state-of-the-art 2D and 3D imaging, allows more robust drug testing. Abstract Follicular lymphoma (FL) is an indolent B cell lymphoproliferative disorder of transformed follicular center B cells, which accounts for 20–30 percent of all non-Hodgkin lymphoma (NHL) cases. Great advances have been made to identify the most relevant targets for precision therapy. However, no relevant models for in vitro studies have been developed or characterized in depth. To this purpose, we generated a 3D cell model from t(14;18)-positive B-NHL cell lines cultured in ultra-low attachment 96-well plates. Morphological features and cell growth behavior were evaluated by classical microscopy (2D imaging) and response to treatment with different drugs was evaluated by a high-content analysis system to determine the robustness of the model. We show that the ultra-low attachment (ULA) method allows the development of regular, spherical and viable ULA-multicellular aggregates of lymphoma cells (MALC). However, discrepancies in the results obtained after 2D imaging analyses on drug-treated ULA-MALC prompted us to develop 3D imaging and specific analyses. We show by using light sheet microscopy and specifically developed 3D imaging algorithms that 3D imaging and dedicated analyses are necessary to characterize morphological properties of 3D models and drug effects. This study proposes a new method, but also imaging tools and informatic solutions, developed for FL necessary for future preclinical studies.
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Hahn A, Bode J, Krüwel T, Kampf T, Buschle LR, Sturm VJF, Zhang K, Tews B, Schlemmer HP, Heiland S, Bendszus M, Ziener CH, Breckwoldt MO, Kurz FT. Gibbs point field model quantifies disorder in microvasculature of U87-glioblastoma. J Theor Biol 2020; 494:110230. [PMID: 32142806 DOI: 10.1016/j.jtbi.2020.110230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 10/28/2019] [Accepted: 03/02/2020] [Indexed: 10/24/2022]
Abstract
Microvascular proliferation in glioblastoma multiforme is a biological key mechanism to facilitate tumor growth and infiltration and a main target for treatment interventions. The vascular architecture can be obtained by Single Plane Illumination Microscopy (SPIM) to evaluate vascular heterogeneity in tumorous tissue. We make use of the Gibbs point field model to quantify the order of regularity in capillary distributions found in the U87 glioblastoma model in a murine model and to compare tumorous and healthy brain tissue. A single model parameter Γ was assigned that is linked to tissue-specific vascular topology through Monte-Carlo simulations. Distributions of the model parameter Γ differ significantly between glioblastoma tissue with mean 〈ΓG〉=2.1±0.4, as compared to healthy brain tissue with mean 〈ΓH〉=4.9±0.4, suggesting that the average Γ-value allows for tissue differentiation. These results may be used for diagnostic magnetic resonance imaging, where it has been shown recently that Γ is linked to tissue-inherent relaxation parameters.
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Affiliation(s)
- Artur Hahn
- Department of Neuroradiology, Heidelberg University Hospital, Im Neuenheimer Feld 400, Heidelberg 69120, Germany; Department of Physics and Astronomy, University of Heidelberg, Im Neuenheimer Feld 226, Heidelberg 69120, Germany
| | - Julia Bode
- Molecular Mechanisms of Tumor Invasion, Schaller Research Group, University of Heidelberg and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg 69120, Germany
| | - Thomas Krüwel
- Molecular Mechanisms of Tumor Invasion, Schaller Research Group, University of Heidelberg and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg 69120, Germany
| | - Thomas Kampf
- Department of Experimental Physics 5, University of Würzburg, Am Hubland, Würzburg 97074, Germany; Department of Neuroradiology, University Hospital Würzburg, Josef-Schneider-Straße 2, Würzburg 97080, Germany
| | - Lukas R Buschle
- Department of Neuroradiology, Heidelberg University Hospital, Im Neuenheimer Feld 400, Heidelberg 69120, Germany; Department of Radiology E010, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Volker J F Sturm
- Department of Neuroradiology, Heidelberg University Hospital, Im Neuenheimer Feld 400, Heidelberg 69120, Germany; Department of Radiology E010, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Ke Zhang
- Department of Radiology E010, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Björn Tews
- Molecular Mechanisms of Tumor Invasion, Schaller Research Group, University of Heidelberg and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg 69120, Germany
| | - Heinz-Peter Schlemmer
- Department of Radiology E010, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Sabine Heiland
- Department of Neuroradiology, Heidelberg University Hospital, Im Neuenheimer Feld 400, Heidelberg 69120, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Im Neuenheimer Feld 400, Heidelberg 69120, Germany
| | - Christian H Ziener
- Department of Neuroradiology, Heidelberg University Hospital, Im Neuenheimer Feld 400, Heidelberg 69120, Germany; Department of Radiology E010, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Michael O Breckwoldt
- Department of Neuroradiology, Heidelberg University Hospital, Im Neuenheimer Feld 400, Heidelberg 69120, Germany; Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Felix T Kurz
- Department of Neuroradiology, Heidelberg University Hospital, Im Neuenheimer Feld 400, Heidelberg 69120, Germany; Department of Radiology E010, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
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Valuchova S, Mikulkova P, Pecinkova J, Klimova J, Krumnikl M, Bainar P, Heckmann S, Tomancak P, Riha K. Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy. eLife 2020; 9:52546. [PMID: 32041682 DOI: 10.7554/elife.52546.sa2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/04/2020] [Indexed: 05/27/2023] Open
Abstract
In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy. We have established reporter lines, cultivation conditions, and imaging protocols for high-resolution microscopy of developing flowers continuously for up to several days. We used multiview imagining to reconstruct a three-dimensional model of a flower at subcellular resolution. We demonstrate the power of this approach by capturing male and female meiosis, asymmetric pollen division, movement of meiotic chromosomes, and unusual restitution mitosis in tapetum cells. This method will enable new avenues of research into plant sexual reproduction.
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Affiliation(s)
- Sona Valuchova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Pavlina Mikulkova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jana Pecinkova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jana Klimova
- IT4Innovations, VSB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Michal Krumnikl
- IT4Innovations, VSB-Technical University of Ostrava, Ostrava, Czech Republic
- Department of Computer Science, FEECS VSB - Technical University of Ostrava, Ostrava, Czech Republic
| | - Petr Bainar
- IT4Innovations, VSB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Karel Riha
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
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Valuchova S, Mikulkova P, Pecinkova J, Klimova J, Krumnikl M, Bainar P, Heckmann S, Tomancak P, Riha K. Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy. eLife 2020; 9:e52546. [PMID: 32041682 PMCID: PMC7012603 DOI: 10.7554/elife.52546] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/04/2020] [Indexed: 12/21/2022] Open
Abstract
In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy. We have established reporter lines, cultivation conditions, and imaging protocols for high-resolution microscopy of developing flowers continuously for up to several days. We used multiview imagining to reconstruct a three-dimensional model of a flower at subcellular resolution. We demonstrate the power of this approach by capturing male and female meiosis, asymmetric pollen division, movement of meiotic chromosomes, and unusual restitution mitosis in tapetum cells. This method will enable new avenues of research into plant sexual reproduction.
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Affiliation(s)
- Sona Valuchova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Pavlina Mikulkova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Jana Pecinkova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Jana Klimova
- IT4InnovationsVSB–Technical University of OstravaOstravaCzech Republic
| | - Michal Krumnikl
- IT4InnovationsVSB–Technical University of OstravaOstravaCzech Republic
- Department of Computer ScienceFEECS VSB – Technical University of OstravaOstravaCzech Republic
| | - Petr Bainar
- IT4InnovationsVSB–Technical University of OstravaOstravaCzech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Karel Riha
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
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Hirvonen LM, Nedbal J, Almutairi N, Phillips TA, Becker W, Conneely T, Milnes J, Cox S, Stürzenbaum S, Suhling K. Lightsheet fluorescence lifetime imaging microscopy with wide-field time-correlated single photon counting. J Biophotonics 2020; 13:e201960099. [PMID: 31661595 PMCID: PMC7065631 DOI: 10.1002/jbio.201960099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 05/22/2023]
Abstract
We report on wide-field time-correlated single photon counting (TCSPC)-based fluorescence lifetime imaging microscopy (FLIM) with lightsheet illumination. A pulsed diode laser is used for excitation, and a crossed delay line anode image intensifier, effectively a single-photon sensitive camera, is used to record the position and arrival time of the photons with picosecond time resolution, combining low illumination intensity of microwatts with wide-field data collection. We pair this detector with the lightsheet illumination technique, and apply it to 3D FLIM imaging of dye gradients in human cancer cell spheroids, and C. elegans.
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Affiliation(s)
- Liisa M. Hirvonen
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | - Jakub Nedbal
- Department of PhysicsKing's College LondonLondonUK
| | - Norah Almutairi
- School of Population Health & Environmental Sciences, Faculty of Life Sciences & MedicineKing's College LondonLondonUK
| | - Thomas A. Phillips
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | | | | | | | - Susan Cox
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | - Stephen Stürzenbaum
- School of Population Health & Environmental Sciences, Faculty of Life Sciences & MedicineKing's College LondonLondonUK
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Girstmair J, Telford MJ. Reinvestigating the early embryogenesis in the flatworm Maritigrella crozieri highlights the unique spiral cleavage program found in polyclad flatworms. EvoDevo 2019; 10:12. [PMID: 31285819 PMCID: PMC6588950 DOI: 10.1186/s13227-019-0126-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/08/2019] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Spiral cleavage is a conserved, early developmental mode found in several phyla of Lophotrochozoans resulting in highly diverse adult body plans. While the cleavage pattern has clearly been broadly conserved, it has also undergone many modifications in various taxa. The precise mechanisms of how different adaptations have altered the ancestral spiral cleavage pattern are an important ongoing evolutionary question, and adequately answering this question requires obtaining a broad developmental knowledge of different spirally cleaving taxa. In flatworms (Platyhelminthes), the spiral cleavage program has been lost or severely modified in most taxa. Polyclad flatworms, however, have retained the pattern up to the 32-cell stage. Here we study early embryogenesis of the cotylean polyclad flatworm Maritigrella crozieri to investigate how closely this species follows the canonical spiral cleavage pattern and to discover any potential deviations from it. RESULTS Using live imaging recordings and 3D reconstructions of embryos, we give a detailed picture of the events that occur during spiral cleavage in M. crozieri. We suggest, contrary to previous observations, that the four-cell stage is a product of unequal cleavages. We show that that the formation of third and fourth micromere quartets is accompanied by strong blebbing events; blebbing also accompanies the formation of micromere 4d. We find an important deviation from the canonical pattern of cleavages with clear evidence that micromere 4d follows an atypical cleavage pattern, so far exclusively found in polyclad flatworms. CONCLUSIONS Our findings highlight that early development in M. crozieri deviates in several important aspects from the canonical spiral cleavage pattern. We suggest that some of our observations extend to polyclad flatworms in general as they have been described in both suborders of the Polycladida, the Cotylea and Acotylea.
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Affiliation(s)
- Johannes Girstmair
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT UK
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Maximilian J. Telford
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT UK
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Daetwyler S, Günther U, Modes CD, Harrington K, Huisken J. Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish. Development 2019; 146:dev173757. [PMID: 30824551 PMCID: PMC6451323 DOI: 10.1242/dev.173757] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/18/2019] [Indexed: 01/14/2023]
Abstract
To quantitatively understand biological processes that occur over many hours or days, it is desirable to image multiple samples simultaneously, and automatically process and analyse the resulting datasets. Here, we present a complete multi-sample preparation, imaging, processing and analysis workflow to determine the development of the vascular volume in zebrafish. Up to five live embryos were mounted and imaged simultaneously over several days using selective plane illumination microscopy (SPIM). The resulting large imagery dataset of several terabytes was processed in an automated manner on a high-performance computer cluster and segmented using a novel segmentation approach that uses images of red blood cells as training data. This analysis yielded a precise quantification of growth characteristics of the whole vascular network, head vasculature and tail vasculature over development. Our multi-sample platform demonstrates effective upgrades to conventional single-sample imaging platforms and paves the way for diverse quantitative long-term imaging studies.
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Affiliation(s)
- Stephan Daetwyler
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Ulrik Günther
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Chair of Scientific Computing for Systems Biology, Faculty of Computer Science, TU Dresden, 01069 Dresden, Germany
| | - Carl D Modes
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Kyle Harrington
- Virtual Technology and Design, University of Idaho, Moscow, ID 83844, USA
| | - Jan Huisken
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA
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Albert-Smet I, Marcos-Vidal A, Vaquero JJ, Desco M, Muñoz-Barrutia A, Ripoll J. Applications of Light-Sheet Microscopy in Microdevices. Front Neuroanat 2019; 13:1. [PMID: 30760983 PMCID: PMC6362405 DOI: 10.3389/fnana.2019.00001] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/09/2019] [Indexed: 11/23/2022] Open
Abstract
Light-sheet fluorescence microscopy (LSFM) has been present in cell biology laboratories for quite some time, mainly as custom-made systems, with imaging applications ranging from single cells (in the micrometer scale) to small organisms (in the millimeter scale). Such microscopes distinguish themselves for having very low phototoxicity levels and high spatial and temporal resolution, properties that make them ideal for a large range of applications. These include the study of cellular dynamics, in particular cellular motion which is essential to processes such as tumor metastasis and tissue development. Experimental setups make extensive use of microdevices (bioMEMS) that provide better control over the substrate environment than traditional cell culture experiments. For example, to mimic in vivo conditions, experiment biochemical dynamics, and trap, move or count cells. Microdevices provide a higher degree of empirical complexity but, so far, most have been designed to be imaged through wide-field or confocal microscopes. Nonetheless, the properties of LSFM render it ideal for 3D characterization of active cells. When working with microdevices, confocal microscopy is more widespread than LSFM even though it suffers from higher phototoxicity and slower acquisition speeds. It is sometimes possible to illuminate with a light-sheet microdevices designed for confocal microscopes. However, these bioMEMS must be redesigned to exploit the full potential of LSFM and image more frequently on a wider scale phenomena such as motion, traction, differentiation, and diffusion of molecules. The use of microdevices for LSFM has extended beyond cell tracking studies into experiments regarding cytometry, spheroid cultures and lab-on-a-chip automation. Due to light-sheet microscopy being in its early stages, a setup of these characteristics demands some degree of optical expertise; and designing three-dimensional microdevices requires facilities, ingenuity, and experience in microfabrication. In this paper, we explore different approaches where light-sheet microscopy can achieve single-cell and subcellular resolution within microdevices, and provide a few pointers on how these experiments may be improved.
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Affiliation(s)
- Ignacio Albert-Smet
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain
| | - Asier Marcos-Vidal
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain
| | - Juan José Vaquero
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain.,Experimental Medicine and Surgery Unit, Instituto de Investigación Sanitaria del Hospital Gregorio Marañón, Madrid, Spain
| | - Manuel Desco
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain.,Experimental Medicine and Surgery Unit, Instituto de Investigación Sanitaria del Hospital Gregorio Marañón, Madrid, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain.,Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Arrate Muñoz-Barrutia
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain.,Experimental Medicine and Surgery Unit, Instituto de Investigación Sanitaria del Hospital Gregorio Marañón, Madrid, Spain
| | - Jorge Ripoll
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain.,Experimental Medicine and Surgery Unit, Instituto de Investigación Sanitaria del Hospital Gregorio Marañón, Madrid, Spain
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Hoffmann S, Mullins L, Buckley C, Rider S, Mullins J. Investigating the RAS can be a fishy business: interdisciplinary opportunities using Zebrafish. Clin Sci (Lond) 2018; 132:2469-2481. [PMID: 30518571 PMCID: PMC6279434 DOI: 10.1042/cs20180721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/02/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023]
Abstract
The renin-angiotensin system (RAS) is highly conserved, and components of the RAS are present in all vertebrates to some degree. Although the RAS has been studied since the discovery of renin, its biological role continues to broaden with the identification and characterization of new peptides. The evolutionarily distant zebrafish is a remarkable model for studying the kidney due to its genetic tractability and accessibility for in vivo imaging. The zebrafish pronephros is an especially useful kidney model due to its structural simplicity yet complex functionality, including capacity for glomerular and tubular filtration. Both the pronephros and mesonephros contain renin-expressing perivascular cells, which respond to RAS inhibition, making the zebrafish an excellent model for studying the RAS. This review summarizes the physiological and genetic tools currently available for studying the zebrafish kidney with regards to functionality of the RAS, using novel imaging techniques such as SPIM microscopy coupled with targeted single cell ablation and synthesis of vasoactive RAS peptides.
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Affiliation(s)
- Scott Hoffmann
- University of Edinburgh/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, The University of Edinburgh, 47, Little France Crescent, Edinburgh EH16 4TJ, U.K
| | - Linda Mullins
- University of Edinburgh/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, The University of Edinburgh, 47, Little France Crescent, Edinburgh EH16 4TJ, U.K
| | - Charlotte Buckley
- University of Edinburgh/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, The University of Edinburgh, 47, Little France Crescent, Edinburgh EH16 4TJ, U.K
| | - Sebastien Rider
- University of Edinburgh/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, The University of Edinburgh, 47, Little France Crescent, Edinburgh EH16 4TJ, U.K
| | - John Mullins
- University of Edinburgh/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, The University of Edinburgh, 47, Little France Crescent, Edinburgh EH16 4TJ, U.K.
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14
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Favre-Bulle IA, Vanwalleghem G, Taylor MA, Rubinsztein-Dunlop H, Scott EK. Cellular-Resolution Imaging of Vestibular Processing across the Larval Zebrafish Brain. Curr Biol 2018; 28:3711-3722.e3. [PMID: 30449665 DOI: 10.1016/j.cub.2018.09.060] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/26/2018] [Accepted: 09/26/2018] [Indexed: 12/20/2022]
Abstract
The vestibular system, which reports on motion and gravity, is essential to postural control, balance, and egocentric representations of movement and space. The motion needed to stimulate the vestibular system complicates studying its circuitry, so we previously developed a method for fictive vestibular stimulation in zebrafish, using optical trapping to apply physical forces to the otoliths. Here, we combine this approach with whole-brain calcium imaging at cellular resolution, delivering a comprehensive map of the brain regions and cellular responses involved in basic vestibular processing. We find responses broadly distributed across the brain, with unique profiles of cellular responses and topography in each region. The most widespread and abundant responses involve excitation that is graded to the stimulus strength. Other responses, localized to the telencephalon and habenulae, show excitation that is only weakly correlated to stimulus strength and that is sensitive to weak stimuli. Finally, numerous brain regions contain neurons that are inhibited by vestibular stimuli, and these neurons are often tightly localized spatially within their regions. By exerting separate control over the left and right otoliths, we explore the laterality of brain-wide vestibular processing, distinguishing between neurons with unilateral and bilateral vestibular sensitivity and revealing patterns whereby conflicting signals from the ears mutually cancel. Our results confirm previously identified vestibular responses in specific regions of the larval zebrafish brain while revealing a broader and more extensive network of vestibular responsive neurons than has previously been described. This provides a departure point for more targeted studies of the underlying functional circuits.
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Affiliation(s)
- Itia A Favre-Bulle
- School of Mathematics and Physics, The University of Queensland, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gilles Vanwalleghem
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael A Taylor
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Ethan K Scott
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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15
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Heap LAL, Vanwalleghem G, Thompson AW, Favre-Bulle IA, Scott EK. Luminance Changes Drive Directional Startle through a Thalamic Pathway. Neuron 2018; 99:293-301.e4. [PMID: 29983325 DOI: 10.1016/j.neuron.2018.06.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/13/2018] [Accepted: 06/07/2018] [Indexed: 01/05/2023]
Abstract
Looming visual stimuli result in escape responses that are conserved from insects to humans. Despite their importance for survival, the circuits mediating visual startle have only recently been explored in vertebrates. Here we show that the zebrafish thalamus is a luminance detector critical to visual escape. Thalamic projection neurons deliver dim-specific information to the optic tectum, and ablations of these projections disrupt normal tectal responses to looms. Without this information, larvae are less likely to escape from dark looming stimuli and lose the ability to escape away from the source of the loom. Remarkably, when paired with an isoluminant loom stimulus to the opposite eye, dimming is sufficient to increase startle probability and to reverse the direction of the escape so that it is toward the loom. We suggest that bilateral comparisons of luminance, relayed from the thalamus to the tectum, facilitate escape responses and are essential for their directionality.
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Affiliation(s)
- Lucy A L Heap
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Gilles Vanwalleghem
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Andrew W Thompson
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Itia A Favre-Bulle
- School of Maths and Physics, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Ethan K Scott
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia; The Queensland Brain Institute, The University of Queensland, St. Lucia, QLD 4072, Australia.
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16
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Laketa V. Microscopy in Infectious Disease Research-Imaging Across Scales. J Mol Biol 2018; 430:2612-25. [PMID: 29908150 DOI: 10.1016/j.jmb.2018.06.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/03/2018] [Accepted: 06/08/2018] [Indexed: 12/18/2022]
Abstract
A comprehensive understanding of host-pathogen interactions requires quantitative assessment of molecular events across a wide range of spatiotemporal scales and organizational complexities. Due to recent technical developments, this is currently only achievable with microscopy. This article is providing a general perspective on the importance of microscopy in infectious disease research, with a focus on new imaging modalities that promise to have a major impact in biomedical research in the years to come. Every major technological breakthrough in light microscopy depends on, and is supported by, advancements in computing and information technologies. Bioimage acquisition and analysis based on machine learning will pave the way toward more robust, automated and objective implementation of new imaging modalities and in biomedical research in general. The combination of novel imaging technologies with machine learning and near-physiological model systems promises to accelerate discoveries and breakthroughs in our understanding of infectious diseases, from basic research all the way to clinical applications.
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Elisa Z, Toon B, De Smedt SC, Katrien R, Kristiaan N, Kevin B. Technical implementations of light sheet microscopy. Microsc Res Tech 2018; 81:941-958. [PMID: 29322581 DOI: 10.1002/jemt.22981] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/14/2017] [Accepted: 12/11/2017] [Indexed: 12/14/2022]
Abstract
Fluorescence-based microscopy is among the most successful methods in biological studies. It played a critical role in the visualization of subcellular structures and in the analysis of complex cellular processes, and it is nowadays commonly employed in genetic and drug screenings. Among the fluorescence-based microscopy techniques, light sheet fluorescence microscopy (LSFM) has shown a quite interesting set of benefits. The technique combines the speed of epi-fluorescence acquisition with the optical sectioning capability typical of confocal microscopes. Its unique configuration allows the excitation of only a thin plane of the sample, thus fast, high resolution imaging deep inside tissues is nowadays achievable. The low peak intensity with which the sample is illuminated diminishes phototoxic effects and decreases photobleaching of fluorophores, ensuring data collection for days with minimal adverse consequences on the sample. It is no surprise that LSFM applications have raised in just few years and the technique has been applied to study a wide variety of samples, from whole organism, to tissues, to cell clusters, and single cells. As a consequence, in recent years numerous set-ups have been developed, each one optimized for the type of sample in use and the requirements of the question at hand. Hereby, we aim to review the most advanced LSFM implementations to assist new LSFM users in the choice of the LSFM set-up that suits their needs best. We also focus on new commercial microscopes and "do-it-yourself" strategies; likewise we review recent designs that allow a swift integration of LSFM on existing microscopes.
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Affiliation(s)
- Zagato Elisa
- Laboratory of General Biochemistry and Physical Pharmacy, Center for Nano- and Biophotonics, Ghent University, Belgium
| | - Brans Toon
- Laboratory of General Biochemistry and Physical Pharmacy, Center for Nano- and Biophotonics, Ghent University, Belgium
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Belgium
| | - Remaut Katrien
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Belgium
| | - Neyts Kristiaan
- Liquid Crystals and Photonics Group, Center for Nano- and Biophotonics, Ghent University, Belgium
| | - Braeckmans Kevin
- Laboratory of General Biochemistry and Physical Pharmacy, Center for Nano- and Biophotonics, Ghent University, Belgium
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18
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Chang BJ, Perez Meza VD, Stelzer EHK. csiLSFM combines light-sheet fluorescence microscopy and coherent structured illumination for a lateral resolution below 100 nm. Proc Natl Acad Sci U S A 2017; 114:4869-74. [PMID: 28438995 DOI: 10.1073/pnas.1609278114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Light-sheet-based fluorescence microscopy (LSFM) features optical sectioning in the excitation process. It minimizes fluorophore bleaching as well as phototoxic effects and provides a true axial resolution. The detection path resembles properties of conventional fluorescence microscopy. Structured illumination microscopy (SIM) is attractive for superresolution because of its moderate excitation intensity, high acquisition speed, and compatibility with all fluorophores. We introduce SIM to LSFM because the combination pushes the lateral resolution to the physical limit of linear SIM. The instrument requires three objective lenses and relies on methods to control two counterpropagating coherent light sheets that generate excitation patterns in the focal plane of the detection lens. SIM patterns with the finest line spacing in the far field become available along multiple orientations. Flexible control of rotation, frequency, and phase shift of the perfectly modulated light sheet are demonstrated. Images of beads prove a near-isotropic lateral resolution of sub-100 nm. Images of yeast endoplasmic reticulum show that coherent structured illumination (csi) LSFM performs with physiologically relevant specimens.
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19
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Pampaloni F, Knuppertz L, Hamann A, Osiewacz HD, Stelzer EHK. Three-Dimensional Live Imaging of Filamentous Fungi with Light Sheet-Based Fluorescence Microscopy (LSFM). Methods Mol Biol 2017; 1563:19-31. [PMID: 28324599 DOI: 10.1007/978-1-4939-6810-7_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We describe a method for the three-dimensional live imaging of filamentous fungi with light sheet-based fluorescence microscopy (LSFM). LSFM provides completely new opportunities to investigate the biology of fungal cells and other microorganisms with high spatial and temporal resolution. As an example, we study the established aging model Podospora anserina. The protocol explains the mounting of the live fungi for the light sheet imaging, the imaging procedure and illustrates basic image processing of data.
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Affiliation(s)
- Francesco Pampaloni
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt am Main, Max-von-Laue-Str. 15, D-60438, Frankfurt am Main, Germany.
| | - Laura Knuppertz
- Institute of Molecular Biosciences and Cluster of Excellence Frankfurt Macromolecular Complexes, Department of Biosciences, Goethe Universität Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Andrea Hamann
- Institute of Molecular Biosciences and Cluster of Excellence Frankfurt Macromolecular Complexes, Department of Biosciences, Goethe Universität Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Heinz D Osiewacz
- Institute of Molecular Biosciences and Cluster of Excellence Frankfurt Macromolecular Complexes, Department of Biosciences, Goethe Universität Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Ernst H K Stelzer
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt am Main, Max-von-Laue-Str. 15, D-60438, Frankfurt am Main, Germany
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20
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Abstract
This chapter introduces the principles and advantages of selective plane illumination microscopy (SPIM) and compares it to commonly used epifluorescence or confocal setups. Due to the low phototoxicity, speed of imaging, high penetration depth, and spatiotemporal resolution, SPIM is predestined for in vivo imaging but can as well be used for in toto analysis of large fixed samples. Key points of light-sheet microscopy are highlighted and discussed priming the investigator to choose the best suitable system from the large collection of possible SPIM setups. Mounting of samples is shown and the demands for data acquisition, processing, handling, and visualization are discussed.
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Affiliation(s)
- D Kromm
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - T Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - J Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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21
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Abstract
Light sheet fluorescent microscopy (LSFM), and in particular its most widespread flavor Selective Plane Illumination Microscopy (SPIM), promises to provide unprecedented insights into developmental dynamics of entire living systems. By combining minimal photo-damage with high imaging speed and sample mounting tailored toward the needs of the specimen, it enables in toto imaging of embryogenesis with high spatial and temporal resolution. Drosophila embryos are particularly well suited for SPIM imaging because the volume of the embryo does not change from the single cell embryo to the hatching larva. SPIM microscopes can therefore image Drosophila embryos embedded in rigid media, such as agarose, from multiple angles every few minutes from the blastoderm stage until hatching. Here, we describe sample mounting strategies to achieve such a recording. We also provide detailed protocols to realize multiview, long-term, time-lapse recording of Drosophila embryos expressing fluorescent markers on the commercially available Zeiss Lightsheet Z.1 microscope and the OpenSPIM.
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Affiliation(s)
- Christopher Schmied
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
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22
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Basu S, Tan YL, Taylor EJR, Laue ED, Lee SF. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localisation Microscopy. Methods Mol Biol 2016; 1431:235-63. [PMID: 27283313 DOI: 10.1007/978-1-4939-3631-1_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single-molecule localisation microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal 'snapshots' of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination and protein labelling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analysing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Srinjan Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Yi Lei Tan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Edward J R Taylor
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Steven F Lee
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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23
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Park OK, Kwak J, Jung YJ, Kim YH, Hong HS, Hwang BJ, Kwon SH, Kee Y. 3D Light-Sheet Fluorescence Microscopy of Cranial Neurons and Vasculature during Zebrafish Embryogenesis. Mol Cells 2015; 38:975-81. [PMID: 26429501 PMCID: PMC4673412 DOI: 10.14348/molcells.2015.0160] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/16/2015] [Accepted: 07/30/2015] [Indexed: 11/27/2022] Open
Abstract
Precise 3D spatial mapping of cells and their connections within living tissues is required to fully understand developmental processes and neural activities. Zebrafish embryos are relatively small and optically transparent, making them the vertebrate model of choice for live in vivo imaging. However, embryonic brains cannot be imaged in their entirety by confocal or two-photon microscopy due to limitations in optical range and scanning speed. Here, we use light-sheet fluorescence microscopy to overcome these limitations and image the entire head of live transgenic zebrafish embryos. We simultaneously imaged cranial neurons and blood vessels during embryogenesis, generating comprehensive 3D maps that provide insight into the coordinated morphogenesis of the nervous system and vasculature during early development. In addition, blood cells circulating through the entire head, vagal and cardiac vasculature were also visualized at high resolution in a 3D movie. These data provide the foundation for the construction of a complete 4D atlas of zebrafish embryogenesis and neural activity.
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Affiliation(s)
- Ok Kyu Park
- Korea Basic Science Institute Chuncheon Center, Chuncheon 200-701,
Korea
| | - Jina Kwak
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701,
Korea
| | - Yoo Jung Jung
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701,
Korea
| | | | | | - Byung Joon Hwang
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 200-701,
Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 200-701,
Korea
| | - Seung-Hae Kwon
- Korea Basic Science Institute Chuncheon Center, Chuncheon 200-701,
Korea
| | - Yun Kee
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701,
Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 200-701,
Korea
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24
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Abstract
Fluorescently labeled structures can be spectrally isolated and imaged at high resolution in living embryos by light sheet microscopy. Multimodal imaging techniques are now needed to put these distinct structures back into the context of the surrounding tissue. We found that the bright-field contrast of unstained specimens in a selective plane illumination microscopy (SPIM) setup can be exploited for in vivo tomographic reconstructions of the three-dimensional anatomy of zebrafish, without causing phototoxicity. We report multimodal imaging of entire zebrafish embryos over several hours of development, as well as segmentation, tracking and automatic registration of individual organs. Summary: Bright-field imaging of unstained specimens during selective plane illumination microscopy can provide in vivo tomographic reconstruction of zebrafish anatomy.
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Affiliation(s)
- Andrea Bassi
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany Politecnico di Milano, Dipartimento di Fisica, Milano 20133, Italy
| | - Benjamin Schmid
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Jan Huisken
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
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25
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Hu YS, Zimmerley M, Li Y, Watters R, Cang H. Single-molecule super-resolution light-sheet microscopy. Chemphyschem 2014; 15:577-86. [PMID: 24615819 DOI: 10.1002/cphc.201300732] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 01/08/2014] [Indexed: 11/10/2022]
Abstract
Single-molecule super-resolution imaging is a new promising tool for investigation of sub-cellular structures. Concurrently, light-sheet microscopy, also known as selective plane illumination microscopy (SPIM), has gained rapid favor with the imaging community in developmental biology due to its fast speed, high contrast, deep penetration, and low phototoxicity. While nearly a dozen reviews thoroughly describe the development of light-sheet microscopy and its technological breakthroughs with a main focus on improving the 3D imaging speed of fish embryos, central nervous system, and other tissues, few have addressed the potential of combining light-sheet microscopy and localization-based super-resolution imaging to achieve sub-diffraction-limited resolution. Adapting light-sheet illumination for single-molecule imaging presents unique challenges for instrumentation and reconstruction algorithms. In this Minireview, we provide an overview of the recent developments that address these challenges. We compare different approaches in super-resolution and light-sheet imaging, address advantages and limitations in each approach, and outline future directions of this emerging field.
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Affiliation(s)
- Ying S Hu
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Rd., La Jolla, CA 92037 (USA)
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26
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Abstract
Light sheet microscopy is an emerging technique allowing comprehensive visualization of dynamic biological processes, at high spatial and temporal resolution without significant damage to the sample by the imaging process itself. It thus lends itself to time-lapse observation of fluorescently labeled molecular markers over long periods of time in a living specimen. In combination with sample rotation light sheet microscopy and in particular its selective plane illumination microscopy (SPIM) flavor, enables imaging of relatively large specimens, such as embryos of animal model organisms, in their entirety. The benefits of SPIM multiview imaging come to the cost of image data postprocessing necessary to deliver the final output that can be analyzed. Here, we provide a set of practical recipes that walk biologists through the complex processes of SPIM data registration, fusion, deconvolution, and time-lapse registration using publicly available open-source tools. We explain, in plain language, the basic principles behind SPIM image-processing algorithms that should enable users to make informed decisions during parameter tuning of the various processing steps applied to their own datasets. Importantly, the protocols presented here are applicable equally to processing of multiview SPIM data from the commercial Zeiss Lightsheet Z.1 microscope and from the open-access SPIM platforms such as OpenSPIM.
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Jemielita M, Taormina MJ, DeLaurier A, Kimmel CB, Parthasarathy R. Comparing phototoxicity during the development of a zebrafish craniofacial bone using confocal and light sheet fluorescence microscopy techniques. J Biophotonics 2013; 6:920-8. [PMID: 23242824 PMCID: PMC3843985 DOI: 10.1002/jbio.201200144] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/31/2012] [Accepted: 11/15/2012] [Indexed: 05/25/2023]
Abstract
The combination of genetically encoded fluorescent proteins and three-dimensional imaging enables cell-type-specific studies of embryogenesis. Light sheet microscopy, in which fluorescence excitation is provided by a plane of laser light, is an appealing approach to live imaging due to its high speed and efficient use of photons. While the advantages of rapid imaging are apparent from recent work, the importance of low light levels to studies of development is not well established. We examine the zebrafish opercle, a craniofacial bone that exhibits pronounced shape changes at early developmental stages, using both spinning disk confocal and light sheet microscopies of fluorescent osteoblast cells. We find normal and aberrant opercle morphologies for specimens imaged with short time intervals using light sheet and spinning disk confocal microscopies, respectively, under equivalent exposure conditions over developmentally-relevant time scales. Quantification of shapes reveals that the differently imaged specimens travel along distinct trajectories in morphological space.
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Affiliation(s)
- Matthew Jemielita
- Department of Physics, 1274 University of Oregon, Eugene, OR, 97403, USA
| | | | - April DeLaurier
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Charles B. Kimmel
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Raghuveer Parthasarathy
- Department of Physics, 1274 University of Oregon, Eugene, OR, 97403, USA
- Materials Science Institute, 1252 University of Oregon, Eugene, OR, 97403, USA
- Institute of Molecular Biology, 1229 University of Oregon, Eugene, OR, 97403, USA
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Desmaison A, Lorenzo C, Rouquette J, Ducommun B, Lobjois V. A versatile sample holder for single plane illumination microscopy. J Microsc 2013; 251:128-32. [PMID: 23691992 DOI: 10.1111/jmi.12051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/23/2013] [Indexed: 02/06/2023]
Abstract
Single Plane Illumination Microscopy is an emerging and powerful technology for live imaging of whole living organisms. However, sample handling that relies on specimen embedding in agarose or gel is often a key limitation, especially for time-lapse monitoring. To address this issue, we developed a new concept for a holder device allowing us to prepare a sample container made of hydrogel. The production process of this holder is based on 3D printing of both a frame and casting devices. The simplicity of production and the advantages of this versatile new sample holder are shown with time-lapse recording of multicellular tumour spheroid growth. More importantly, we also show that cell division is not impaired in contrast to what is observed with gel embedding. The benefit of this new holder for other sample types, applications and experiments remains to be evaluated, but this innovative concept of fully customizable sample holder preparation potentially represents a major step forward to facilitate the large diffusion of single plane illumination microscopy technology.
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