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Strobl F, Ratke J, Krämer F, Utta A, Becker S, Stelzer EHK. Next generation marker-based vector concepts for rapid and unambiguous identification of single and double homozygous transgenic organisms. Biol Open 2023; 12:bio060015. [PMID: 37855381 PMCID: PMC10602009 DOI: 10.1242/bio.060015] [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: 05/17/2023] [Accepted: 08/15/2023] [Indexed: 10/20/2023] Open
Abstract
For diploid model organisms, the actual transgenesis processes require subsequent periods of transgene management, which are challenging in emerging model organisms due to the lack of suitable methodology. We used the red flour beetle Tribolium castaneum, a stored-grain pest, to perform a comprehensive functional evaluation of our AClashOfStrings (ACOS) and the combined AGameOfClones/AClashOfStrings (AGOC/ACOS) vector concepts, which use four clearly distinguishable markers to provide full visual control over up to two independent transgenes. We achieved comprehensive statistical validation of our approach by systematically creating seventeen novel single and double homozygous sublines intended for fluorescence live imaging, including several sublines in which the microtubule cytoskeleton is labeled. During the mating procedures, we genotyped more than 20,000 individuals in less than 80 working hours, which corresponds to about 10 to 15 s per individual. We also confirm the functionality of our combined concept in two double transgene special cases, i.e. integration of both transgenes in close proximity on the same chromosome and integration of one transgene on the X allosome. Finally, we discuss our vector concepts regarding performance, genotyping accuracy, throughput, resource saving potential, fluorescent protein choice, modularity, adaptation to other diploid model organisms and expansion capability.
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Affiliation(s)
- Frederic Strobl
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Julia Ratke
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Franziska Krämer
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Ana Utta
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Sigrun Becker
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Ernst H. K. Stelzer
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
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Burcklen MA, Galland F, Le Goff L. Optimizing sampling for surface localization in 3D-scanning microscopy. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2022; 39:1479-1488. [PMID: 36215593 DOI: 10.1364/josaa.460077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/06/2022] [Indexed: 06/16/2023]
Abstract
3D-scanning fluorescence imaging of living tissue is in demand for less phototoxic acquisition process. For the imaging of biological surfaces, adaptive and sparse scanning schemes have been proven to efficiently reduce the light dose by concentrating acquisitions around the surface. In this paper, we focus on optimizing the scanning scheme at a constant photon budget, when the problem is to estimate the position of a biological surface whose intensity profile is modeled as a Gaussian shape. We propose an approach based on the Cramér-Rao bound to optimize the positions and number of scanning points, assuming signal-dependant Gaussian noise. We show that, in the case of regular sampling, the optimization problem can be reduced to a few parameters, allowing us to define quasi-optimal acquisition strategies, first when no prior knowledge of the surface location is available and then when the user has a prior on this location.
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Khoshravesh R, Hoffmann N, Hanson DT. Leaf microscopy applications in photosynthesis research: identifying the gaps. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1868-1893. [PMID: 34986250 DOI: 10.1093/jxb/erab548] [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: 08/23/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure-function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.
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Affiliation(s)
| | - Natalie Hoffmann
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - David T Hanson
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
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4
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Zeng C, Chen Z, Yang H, Fan Y, Fei L, Chen X, Zhang M. Advanced high resolution three-dimensional imaging to visualize the cerebral neurovascular network in stroke. Int J Biol Sci 2022; 18:552-571. [PMID: 35002509 PMCID: PMC8741851 DOI: 10.7150/ijbs.64373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/28/2021] [Indexed: 11/05/2022] Open
Abstract
As an important method to accurately and timely diagnose stroke and study physiological characteristics and pathological mechanism in it, imaging technology has gone through more than a century of iteration. The interaction of cells densely packed in the brain is three-dimensional (3D), but the flat images brought by traditional visualization methods show only a few cells and ignore connections outside the slices. The increased resolution allows for a more microscopic and underlying view. Today's intuitive 3D imagings of micron or even nanometer scale are showing its essentiality in stroke. In recent years, 3D imaging technology has gained rapid development. With the overhaul of imaging mediums and the innovation of imaging mode, the resolution has been significantly improved, endowing researchers with the capability of holistic observation of a large volume, real-time monitoring of tiny voxels, and quantitative measurement of spatial parameters. In this review, we will summarize the current methods of high-resolution 3D imaging applied in stroke.
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Affiliation(s)
- Chudai Zeng
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Zhuohui Chen
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Haojun Yang
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Yishu Fan
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Lujing Fei
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Xinghang Chen
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Mengqi Zhang
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
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5
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Abouakil F, Meng H, Burcklen MA, Rigneault H, Galland F, LeGoff L. An adaptive microscope for the imaging of biological surfaces. LIGHT, SCIENCE & APPLICATIONS 2021; 10:210. [PMID: 34620828 PMCID: PMC8497591 DOI: 10.1038/s41377-021-00649-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/20/2021] [Indexed: 05/05/2023]
Abstract
Scanning fluorescence microscopes are now able to image large biological samples at high spatial and temporal resolution. This comes at the expense of an increased light dose which is detrimental to fluorophore stability and cell physiology. To highly reduce the light dose, we designed an adaptive scanning fluorescence microscope with a scanning scheme optimized for the unsupervised imaging of cell sheets, which underly the shape of many embryos and organs. The surface of the tissue is first delineated from the acquisition of a very small subset (~0.1%) of sample space, using a robust estimation strategy. Two alternative scanning strategies are then proposed to image the tissue with an improved photon budget, without loss in resolution. The first strategy consists in scanning only a thin shell around the estimated surface of interest, allowing high reduction of light dose when the tissue is curved. The second strategy applies when structures of interest lie at the cell periphery (e.g. adherens junctions). An iterative approach is then used to propagate scanning along cell contours. We demonstrate the benefit of our approach imaging live epithelia from Drosophila melanogaster. On the examples shown, both approaches yield more than a 20-fold reduction in light dose -and up to more than 80-fold- compared to a full scan of the volume. These smart-scanning strategies can be easily implemented on most scanning fluorescent imaging modality. The dramatic reduction in light exposure of the sample should allow prolonged imaging of the live processes under investigation.
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Affiliation(s)
- Faris Abouakil
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Turing Center for Living Systems, Marseille, France
| | - Huicheng Meng
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Turing Center for Living Systems, Marseille, France
| | - Marie-Anne Burcklen
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Turing Center for Living Systems, Marseille, France
| | - Hervé Rigneault
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Turing Center for Living Systems, Marseille, France
| | - Frédéric Galland
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Turing Center for Living Systems, Marseille, France.
| | - Loïc LeGoff
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Turing Center for Living Systems, Marseille, France.
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6
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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.
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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
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7
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Yordanov S, Neuhaus K, Hartmann R, Díaz-Pascual F, Vidakovic L, Singh PK, Drescher K. Single-objective high-resolution confocal light sheet fluorescence microscopy for standard biological sample geometries. BIOMEDICAL OPTICS EXPRESS 2021; 12:3372-3391. [PMID: 34221666 PMCID: PMC8221969 DOI: 10.1364/boe.420788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/22/2021] [Accepted: 04/19/2021] [Indexed: 06/13/2023]
Abstract
Three-dimensional fluorescence-based imaging of living cells and organisms requires the sample to be exposed to substantial excitation illumination energy, typically causing phototoxicity and photobleaching. Light sheet fluorescence microscopy dramatically reduces phototoxicity, yet most implementations are limited to objective lenses with low numerical aperture and particular sample geometries that are built for specific biological systems. To overcome these limitations, we developed a single-objective light sheet fluorescence system for biological imaging based on axial plane optical microscopy and digital confocal slit detection, using either Bessel or Gaussian beam shapes. Compared to spinning disk confocal microscopy, this system displays similar optical resolution, but a significantly reduced photobleaching at the same signal level. This single-objective light sheet technique is built as an add-on module for standard research microscopes and the technique is compatible with high-numerical aperture oil immersion objectives and standard samples mounted on coverslips. We demonstrate the performance of this technique by imaging three-dimensional dynamic processes, including bacterial biofilm dispersal, the response of biofilms to osmotic shocks, and macrophage phagocytosis of bacterial cells.
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Affiliation(s)
- Stoyan Yordanov
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
- Equal contribution
| | - Konstantin Neuhaus
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Renthof 5, 35037 Marburg, Germany
- Equal contribution
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Francisco Díaz-Pascual
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Lucia Vidakovic
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Praveen K. Singh
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Renthof 5, 35037 Marburg, Germany
- Biozentrum, University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
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8
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Jonkman J, Brown CM, Wright GD, Anderson KI, North AJ. Tutorial: guidance for quantitative confocal microscopy. Nat Protoc 2020. [PMID: 32235926 DOI: 10.1038/s41596-020-0313-319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
When used appropriately, a confocal fluorescence microscope is an excellent tool for making quantitative measurements in cells and tissues. The confocal microscope's ability to block out-of-focus light and thereby perform optical sectioning through a specimen allows the researcher to quantify fluorescence with very high spatial precision. However, generating meaningful data using confocal microscopy requires careful planning and a thorough understanding of the technique. In this tutorial, the researcher is guided through all aspects of acquiring quantitative confocal microscopy images, including optimizing sample preparation for fixed and live cells, choosing the most suitable microscope for a given application and configuring the microscope parameters. Suggestions are offered for planning unbiased and rigorous confocal microscope experiments. Common pitfalls such as photobleaching and cross-talk are addressed, as well as several troubling instrumentation problems that may prevent the acquisition of quantitative data. Finally, guidelines for analyzing and presenting confocal images in a way that maintains the quantitative nature of the data are presented, and statistical analysis is discussed. A visual summary of this tutorial is available as a poster (https://doi.org/10.1038/s41596-020-0307-7).
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Affiliation(s)
- James Jonkman
- Advanced Optical Microscopy Facility (AOMF), University Health Network, Toronto, Ontario, Canada.
| | - Claire M Brown
- Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada
| | - Graham D Wright
- A*STAR Microscopy Platform (AMP), Skin Research Institute of Singapore, A*STAR, Singapore, Singapore
| | - Kurt I Anderson
- Crick Advanced Light Microscopy Facility (CALM), The Francis Crick Institute, London, UK
| | - Alison J North
- Bio-Imaging Resource Center, The Rockefeller University, New York, NY, USA
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Keomanee-Dizon K, Fraser SE, Truong TV. A versatile, multi-laser twin-microscope system for light-sheet imaging. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:053703. [PMID: 32486724 PMCID: PMC7255815 DOI: 10.1063/1.5144487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/28/2020] [Indexed: 05/25/2023]
Abstract
Light-sheet microscopy offers faster imaging and reduced phototoxicity in comparison to conventional point-scanning microscopy, making it a preferred technique for imaging biological dynamics for durations of hours or days. Such extended imaging sessions pose a challenge, as it reduces the number of specimens that can be imaged in a given day. Here, we present a versatile light-sheet imaging instrument that combines two independently controlled microscope-twins, built so that they can share an ultrafast near-infrared laser and a bank of continuous-wave visible lasers, increasing the throughput and decreasing the cost. To permit a wide variety of specimens to be imaged, each microscope-twin provides flexible imaging parameters, including (i) operation in one-photon and/or two-photon excitation modes, (ii) delivery of one to three light-sheets via a trio of orthogonal excitation arms, (iii) sub-micron to micron imaging resolution, (iv) multicolor compatibility, and (v) upright (with provision for inverted) detection geometry. We offer a detailed description of the twin-microscope design to aid instrument builders who wish to construct and use similar systems. We demonstrate the instrument's versatility for biological investigation by performing fast imaging of the beating heart in an intact zebrafish embryo, deep imaging of thick patient-derived tumor organoids, and gentle whole-brain imaging of neural activity in behaving larval zebrafish.
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Affiliation(s)
- Kevin Keomanee-Dizon
- Translational Imaging Center, Dornsife College of Letters, Arts and Sciences, and Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - Scott E. Fraser
- Translational Imaging Center, Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Thai V. Truong
- Translational Imaging Center, Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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10
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Jonkman J, Brown CM, Wright GD, Anderson KI, North AJ. Tutorial: guidance for quantitative confocal microscopy. Nat Protoc 2020; 15:1585-1611. [DOI: 10.1038/s41596-020-0313-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 02/10/2020] [Indexed: 01/04/2023]
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11
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Xiong B, Han X, Wu J, Xie H, Dai Q. Improving axial resolution of Bessel beam light-sheet fluorescence microscopy by photobleaching imprinting. OPTICS EXPRESS 2020; 28:9464-9476. [PMID: 32225553 DOI: 10.1364/oe.388808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
Light-sheet microscopy has been widely used in high-speed fluorescence imaging with low phototoxicity, while the trade-off between the field-of-view and optical sectioning capability limits its application in large-scale imaging. Although Bessel beam light-sheet microscopy greatly enhances the light-sheet length with the self-healing ability, it suffers from the strong side-lobe effect. To solve these problems, we introduce the photobleaching imprinting technique in Bessel beam light-sheet microscopy. By extracting the non-linear photobleaching-induced fluorescence decay, we get rid of the large concentric side lobe structures of the Bessel beam to achieve uniform isotropic resolution across a large field-of-view for large-scale fluorescence imaging. Both numerical simulations and experimental results on various samples are demonstrated to show our enhanced resolution and contrast over traditional Bessel-beam light-sheet microscopy.
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Su Y, Wei L, Tan H, Li J, Li W, Fu L, Wang T, Kang L, Yao XS. Optical coherence tomography as a noninvasive 3D real time imaging tool for the rapid evaluation of phenotypic variations in insect embryonic development. JOURNAL OF BIOPHOTONICS 2020; 13:e201960047. [PMID: 31682322 DOI: 10.1002/jbio.201960047] [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: 07/18/2019] [Revised: 09/24/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
Noninvasive visualization of embryos at different development stages is crucial for the understanding of the basic developmental biology. It is therefore desirable to have an imaging tool capable of rapidly evaluating the effects of gene manipulation or genome editing in developing embryos for the studies of gene functions and genetic engineering. Here, we propose and demonstrate a novel use of optical coherence tomography (OCT) to noninvasively exam the embryonic development of the migratory locusts in real time with 3-dimensional (3D) view capability. In particular, we obtain the sufficiently high spatial resolution tomographic 2D and 3D images of live locust embryos throughout their development processes. We show that not only we are able to noninvasively observe all previously known forms of blastokinesis as an embryo develops, such as anatrepsis, katatrepsis, revolution, rotation and diapauses, and determine their precise occurring time or duration, but also discover an unreported rotation form we named "twist." In addition, with the OCT images we determined the exact occurring time of diapauses of the locusts from Tibetan plateau for the first time. Finally, we demonstrate that OCT systems can be used to rapidly capture the development defects of genetically modified embryos in which certain genes essential for embryonic development were suppressed by RNA interference. Our work shows that OCT is an enabling imaging tool with sufficient spatial resolution for the rapid evaluation of embryonic variations of small animals.
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Affiliation(s)
- Ya Su
- Photonics Information Innovation Center, Hebei Provincial Center for Optical Sensing Innovations, College of Physics Science & Technology, Hebei University, Baoding, China
| | - Liya Wei
- College of Life Sciences, Hebei University, Baoding, China
| | - Hao Tan
- Photonics Information Innovation Center, Hebei Provincial Center for Optical Sensing Innovations, College of Physics Science & Technology, Hebei University, Baoding, China
| | - Jing Li
- College of Life Sciences, Hebei University, Baoding, China
| | - Wenping Li
- Photonics Information Innovation Center, Hebei Provincial Center for Optical Sensing Innovations, College of Physics Science & Technology, Hebei University, Baoding, China
| | - Lei Fu
- Photonics Information Innovation Center, Hebei Provincial Center for Optical Sensing Innovations, College of Physics Science & Technology, Hebei University, Baoding, China
| | - Tongxin Wang
- College of Life Sciences, Hebei University, Baoding, China
| | - Le Kang
- College of Life Sciences, Hebei University, Baoding, China
| | - X Steve Yao
- Photonics Information Innovation Center, Hebei Provincial Center for Optical Sensing Innovations, College of Physics Science & Technology, Hebei University, Baoding, China
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13
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Pied N, Wodrich H. Imaging the adenovirus infection cycle. FEBS Lett 2019; 593:3419-3448. [PMID: 31758703 DOI: 10.1002/1873-3468.13690] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022]
Abstract
Incoming adenoviruses seize control of cytosolic transport mechanisms to relocate their genome from the cell periphery to specialized sites in the nucleoplasm. The nucleus is the site for viral gene expression, genome replication, and the production of progeny for the next round of infection. By taking control of the cell, adenoviruses also suppress cell-autonomous immunity responses. To succeed in their production cycle, adenoviruses rely on well-coordinated steps, facilitated by interactions between viral proteins and cellular factors. Interactions between virus and host can impose remarkable morphological changes in the infected cell. Imaging adenoviruses has tremendously influenced how we delineate individual steps in the viral life cycle, because it allowed the development of specific optical markers to label these morphological changes in space and time. As technology advances, innovative imaging techniques and novel tools for specimen labeling keep uncovering previously unseen facets of adenovirus biology emphasizing why imaging adenoviruses is as attractive today as it was in the past. This review will summarize past achievements and present developments in adenovirus imaging centered on fluorescence microscopy approaches.
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Affiliation(s)
- Noémie Pied
- CNRS UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, France
| | - Harald Wodrich
- CNRS UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, France
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14
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Isaacson D, McCreedy D, Calvert M, Shen J, Sinclair A, Cao M, Li Y, McDevitt T, Cunha G, Baskin L. Imaging the developing human external and internal urogenital organs with light sheet fluorescence microscopy. Differentiation 2019; 111:12-21. [PMID: 31634681 DOI: 10.1016/j.diff.2019.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/07/2019] [Accepted: 09/10/2019] [Indexed: 10/25/2022]
Abstract
Technological advances in three-dimensional (3D) reconstruction techniques have previously enabled paradigm shifts in our understanding of human embryonic and fetal development. Light sheet fluorescence microscopy (LSFM) is a recently-developed technique that uses thin planes of light to optically section whole-mount cleared and immunolabeled biologic specimens. The advent of commercially-available light sheet microscopes has facilitated a new generation of research into protein localization and tissue dynamics at extremely high resolution. Our group has applied LSFM to study developing human fetal external genitalia, internal genitalia and kidneys. This review describes LSFM and presents our group's technique for preparing, clearing, immunostaining and imaging human fetal urogenital specimens. We then present light sheet images and videos of each element of the developing human urogenital system. To the extent of our knowledge, the work conducted by our laboratory represents the first description of a method for performing LSFM on the full human urogenital system during the embryonic and fetal periods.
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Affiliation(s)
- Dylan Isaacson
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Dylan McCreedy
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Meredith Calvert
- Histology and Light Microscopy Core, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Joel Shen
- CytomX Therapeutics, Inc. South San Francisco, CA, USA
| | - Adriane Sinclair
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Mei Cao
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Yi Li
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Todd McDevitt
- Department of Bioengineering and Therapeutic Sciences, J. David Gladstone Institutes, San Francisco, CA, USA; Institute of Cardiovascular Disease, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Gerald Cunha
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Laurence Baskin
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Division of Pediatric Urology, University of California San Francisco Benioff Children's Hospital, San Francisco, CA, USA
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15
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Booij TH, Price LS, Danen EHJ. 3D Cell-Based Assays for Drug Screens: Challenges in Imaging, Image Analysis, and High-Content Analysis. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2019; 24:615-627. [PMID: 30817892 PMCID: PMC6589915 DOI: 10.1177/2472555219830087] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/17/2019] [Accepted: 01/21/2019] [Indexed: 12/13/2022]
Abstract
The introduction of more relevant cell models in early preclinical drug discovery, combined with high-content imaging and automated analysis, is expected to increase the quality of compounds progressing to preclinical stages in the drug development pipeline. In this review we discuss the current switch to more relevant 3D cell culture models and associated challenges for high-throughput screening and high-content analysis. We propose that overcoming these challenges will enable front-loading the drug discovery pipeline with better biology, extracting the most from that biology, and, in general, improving translation between in vitro and in vivo models. This is expected to reduce the proportion of compounds that fail in vivo testing due to a lack of efficacy or to toxicity.
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Affiliation(s)
- Tijmen H. Booij
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- NEXUS Personalized Health Technologies, ETH Zürich, Switzerland
| | - Leo S. Price
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- OcellO B.V., Leiden, The Netherlands
| | - Erik H. J. Danen
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
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16
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Bai C, Liu C, Jia H, Peng T, Min J, Lei M, Yu X, Yao B. Compressed Blind Deconvolution and Denoising for Complementary Beam Subtraction Light-Sheet Fluorescence Microscopy. IEEE Trans Biomed Eng 2019; 66:2979-2989. [PMID: 30794159 DOI: 10.1109/tbme.2019.2899583] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE The side-lobes of a Bessel beam (BB) create a severe out-of-focus background in scanning light-sheet fluorescence microscopy, thereby extremely limiting the axial resolution. The complementary beam subtraction (CBS) method can significantly reduce the out-of-focus background by double scanning a BB and its complementary beam. However, the blurring and noise caused by the system instability during the double scanning and subtraction operations degrade the image quality significantly. Therefore, we propose a compressed blind deconvolution and denoising (CBDD) method that solves this problem. METHODS We use a unified formulation that comprehensively takes advantage of multiple compressed sensing reconstructions and blind sparse representation. RESULTS The simulations and experiments were performed using the microbeads and model organisms to verify the effectiveness of the proposed method. Compared with the CBS light-sheet method, the proposed CBDD algorithm achieved the gain improvement in the axial and lateral resolution of about 1.81 and 2.22 times, respectively, while the average signal-to-noise ratio (SNR) was increased by about 3 dB. CONCLUSION Accordingly, the proposed method can suppress the noise level, enhance the SNR, and recover the degraded resolution simultaneously. SIGNIFICANCE The obtained results demonstrate the proposed CBDD algorithm is well suited to improve the imaging performance of the CBS light-sheet fluorescence microscopy.
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17
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Friedmann KS, Bozem M, Hoth M. Calcium signal dynamics in T lymphocytes: Comparing in vivo and in vitro measurements. Semin Cell Dev Biol 2019; 94:84-93. [PMID: 30630031 DOI: 10.1016/j.semcdb.2019.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/18/2018] [Accepted: 01/05/2019] [Indexed: 02/06/2023]
Abstract
Amplitude and kinetics of intracellular Ca2+ signals ([Ca2+]int) determine many immune cell functions. To mimic in vivo changes of [Ca2+]int in human immune cells, two approaches may be best suited: 1) Analyze primary human immune cells taken from blood under conditions resembling best physiological or pathophysiological conditions. 2.) Analyze the immune system in vivo or ex vivo in explanted tissue from small vertebrate animals, such as mice. With the help of genetically encoded Ca2+ indicators and intravital microscopy, [Ca2+]int have been investigated in murine T lymphocytes (T cells) in vivo during the last five years and in explanted lymph node (LN) during the last 10 years. There are several important reasons to compare [Ca2+]int measured in primary murine T lymphocytes in vivo and in vitro with [Ca2+]int measured in primary human T lymphocytes in vitro. First, how do human and murine data compare? Second, how do in vivo and in vitro data compare? Third, can in vitro data predict in vivo data? The last point is particularly important considering the many technical challenges that limit in vivo measurements and to reduce the number of animals sacrificed. This review summarizes and compares the results of the available publications on in vivo and in vitro [Ca2+]int measurements in T lymphocytes stimulated focally by antigen-presenting cells (APC) after forming an immunological synapse.
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Affiliation(s)
- Kim S Friedmann
- Department of Biophysics, Center for Integrative Physiology and Molecular Medicine, Medical Faculty, Saarland University, Homburg, Germany
| | - Monika Bozem
- Department of Biophysics, Center for Integrative Physiology and Molecular Medicine, Medical Faculty, Saarland University, Homburg, Germany
| | - Markus Hoth
- Department of Biophysics, Center for Integrative Physiology and Molecular Medicine, Medical Faculty, Saarland University, Homburg, Germany.
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18
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Backes CS, Friedmann KS, Mang S, Knörck A, Hoth M, Kummerow C. Natural killer cells induce distinct modes of cancer cell death: Discrimination, quantification, and modulation of apoptosis, necrosis, and mixed forms. J Biol Chem 2018; 293:16348-16363. [PMID: 30190323 DOI: 10.1074/jbc.ra118.004549] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/21/2018] [Indexed: 12/13/2022] Open
Abstract
Immune therapy of cancer is among the most promising recent advances in medicine. Whether the immune system can keep cancer in check depends on, among other factors, the efficiency of immune cells to recognize and eliminate cancer cells. We describe a time-resolved single-cell assay that reports the quality, quantity, and kinetics of target cell death induced by single primary human natural killer (NK) cells. The assay reveals that single NK cells induce cancer cell death by apoptosis and necrosis but also by mixed forms. Inhibition of either one of the two major cytotoxic pathways, perforin/granzyme release or FasL/FasR interaction, unmasked the parallel activity of the other one. Ca2+ influx through Orai channels is important for tuning killer cell function. We found that the apoptosis/necrosis ratio of cancer cell death by NK cells is controlled by the magnitude of Ca2+ entry and furthermore by the relative concentrations of perforin and granzyme B. The possibility to change the apoptosis/necrosis ratio employed by NK cells offers an intriguing possibility to modulate the immunogenicity of the tumor microenvironment.
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Affiliation(s)
- Christian S Backes
- From the Department of Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, 66421 Homburg, Germany
| | - Kim S Friedmann
- From the Department of Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, 66421 Homburg, Germany
| | - Sebastian Mang
- From the Department of Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, 66421 Homburg, Germany
| | - Arne Knörck
- From the Department of Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, 66421 Homburg, Germany
| | - Markus Hoth
- From the Department of Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, 66421 Homburg, Germany
| | - Carsten Kummerow
- From the Department of Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, 66421 Homburg, Germany
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19
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Strobl F, Ross JA, Stelzer EHK. Non-lethal genotyping of Tribolium castaneum adults using genomic DNA extracted from wing tissue. PLoS One 2017; 12:e0182564. [PMID: 28800588 PMCID: PMC5553768 DOI: 10.1371/journal.pone.0182564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/20/2017] [Indexed: 01/11/2023] Open
Abstract
The red flour beetle Tribolium castaneum has become the second most important insect model organism and is frequently used in developmental biology, genetics and pest-associated research. Consequently, the methodological arsenal increases continuously, but many routinely applied techniques for Drosophila melanogaster and other insect species are still unavailable. For example, a protocol for non-lethal genotyping has not yet been adapted but is particularly useful when individuals with known genotypes are required for downstream experiments. In this study, we present a workflow for non-lethal genotyping of T. castaneum adults based on extracting genomic DNA from wing tissue. In detail, we describe a convenient procedure for wing dissection and a custom method for wing digestion that allows PCR-based genotyping of up to fifty adults in less than an afternoon with a success rate of about 86%. The amount of template is sufficient for up to ten reactions while viability and fertility of the beetles are preserved. We prove the applicability of our protocol by genotyping the white / scarlet gene pair alleles from the black-eyed San Bernadino wild-type and white-eyed Pearl recessive mutant strains spanning four generations. Non-lethal genotyping has the potential to improve and accelerate many workflows: Firstly, during the establishment process of homozygous cultures or during stock keeping of cultures that carry recessively lethal alleles, laborious test crossing is replaced by non-lethal genotyping. Secondly, in genome engineering assays, non-lethal genotyping allows the identification of appropriate founders before they are crossed against wild-types, narrowing the efforts down to only the relevant individuals. Thirdly, non-lethal genotyping simplifies experimental strategies, in which genotype and behavior should be correlated, since the genetic configuration of potential individuals can be determined before the actual behavior assays is performed.
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Affiliation(s)
- Frederic Strobl
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt–Macromolecular Complexes (CEF–MC), Goethe Universität–Frankfurt am Main (Campus Riedberg), Max-von-Laue-Straße 15, Frankfurt am Main–Germany
| | - J. Alexander Ross
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt–Macromolecular Complexes (CEF–MC), Goethe Universität–Frankfurt am Main (Campus Riedberg), Max-von-Laue-Straße 15, Frankfurt am Main–Germany
| | - Ernst H. K. Stelzer
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt–Macromolecular Complexes (CEF–MC), Goethe Universität–Frankfurt am Main (Campus Riedberg), Max-von-Laue-Straße 15, Frankfurt am Main–Germany
- * E-mail:
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