151
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Calovi S, Soria FN, Tønnesen J. Super-resolution STED microscopy in live brain tissue. Neurobiol Dis 2021; 156:105420. [PMID: 34102277 DOI: 10.1016/j.nbd.2021.105420] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
STED microscopy is one of several fluorescence microscopy techniques that permit imaging at higher spatial resolution than what the diffraction-limit of light dictates. STED imaging is unique among these super-resolution modalities in being a beam-scanning microscopy technique based on confocal or 2-photon imaging, which provides the advantage of superior optical sectioning in thick samples. Compared to the other super-resolution techniques that are based on widefield microscopy, this makes STED particularly suited for imaging inside live brain tissue, such as in slices or in vivo. Notably, the 50 nm resolution provided by STED microscopy enables analysis of neural morphologies that conventional confocal and 2-photon microscopy approaches cannot resolve, including all-important synaptic structures. Over the course of the last 20 years, STED microscopy has undergone extensive developments towards ever more versatile use, and has facilitated remarkable neurophysiological discoveries. The technique is still not widely adopted for live tissue imaging, even though one of its particular strengths is exactly in resolving the nanoscale dynamics of synaptic structures in brain tissue, as well as in addressing the complex morphologies of glial cells, and revealing the intricate structure of the brain extracellular space. Not least, live tissue STED microscopy has so far hardly been applied in settings of pathophysiology, though also here it shows great promise for providing new insights. This review outlines the technical advantages of STED microscopy for imaging in live brain tissue, and highlights key neurobiological findings brought about by the technique.
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Affiliation(s)
- Stefano Calovi
- Laboratory of Molecular Pharmacology, Institute of Experimental Medicine, Budapest, Hungary; János Szentágothai Doctoral School, Semmelweis University, Budapest, Hungary; Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Federico N Soria
- Achucarro Basque Center for Neuroscience, Leioa, Spain; Department of Neuroscience, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jan Tønnesen
- Achucarro Basque Center for Neuroscience, Leioa, Spain; Department of Neuroscience, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain.
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152
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Kandel ME, Kim E, Lee YJ, Tracy G, Chung HJ, Popescu G. Multiscale Assay of Unlabeled Neurite Dynamics Using Phase Imaging with Computational Specificity. ACS Sens 2021; 6:1864-1874. [PMID: 33882232 PMCID: PMC8815662 DOI: 10.1021/acssensors.1c00100] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Primary neuronal cultures have been widely used to study neuronal morphology, neurophysiology, neurodegenerative processes, and molecular mechanism of synaptic plasticity underlying learning and memory. However, the unique behavioral properties of neurons make them challenging to study, with phenotypic differences expressed as subtle changes in neuronal arborization rather than easy-to-assay features such as cell count. The need to analyze morphology, growth, and intracellular transport has motivated the development of increasingly sophisticated microscopes and image analysis techniques. Due to its high-contrast, high-specificity output, many assays rely on confocal fluorescence microscopy, genetic methods, or antibody staining techniques. These approaches often limit the ability to measure quantitatively dynamic activity such as intracellular transport and growth. In this work, we describe a method for label-free live-cell cell imaging with antibody staining specificity by estimating the associated fluorescence signals via quantitative phase imaging and deep convolutional neural networks. This computationally inferred fluorescence image is then used to generate a semantic segmentation map, annotating subcellular compartments of live unlabeled neural cultures. These synthetic fluorescence maps were further applied to study the time-lapse development of hippocampal neurons, highlighting the relationships between the cellular dry mass production and the dynamic transport activity within the nucleus and neurites. Our implementation provides a high-throughput strategy to analyze neural network arborization dynamically, with high specificity and without the typical phototoxicity and photobleaching limitations associated with fluorescent markers.
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Affiliation(s)
- Mikhail E Kandel
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Eunjae Kim
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Young Jae Lee
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Gregory Tracy
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, United States
| | - Hee Jung Chung
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, United States
| | - Gabriel Popescu
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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153
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Nguyen DP, Nguyen HTH, Do LH. Tools and Methods for Investigating Synthetic Metal-Catalyzed Reactions in Living Cells. ACS Catal 2021; 11:5148-5165. [PMID: 34824879 PMCID: PMC8612649 DOI: 10.1021/acscatal.1c00438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although abiotic catalysts are capable of promoting numerous new-to-nature reactions, only a small subset has so far been successfully integrated into living systems. Research in intracellular catalysis requires an interdisciplinary approach that takes advantage of both chemical and biological tools as well as state-of-the-art instrumentations. In this perspective, we will focus on the techniques that have made studying metal-catalyzed reactions in cells possible using representative examples from the literature. Although the lack of quantitative data in vitro and in vivo has somewhat limited progress in the catalyst development process, recent advances in characterization methods should help overcome some of these deficiencies. Given its tremendous potential, we believe that intracellular catalysis will play a more prominent role in the development of future biotechnologies and therapeutics.
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Affiliation(s)
- Dat P. Nguyen
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
| | - Huong T. H. Nguyen
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
| | - Loi H. Do
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
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154
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Hagen GM, Bendesky J, Machado R, Nguyen TA, Kumar T, Ventura J. Fluorescence microscopy datasets for training deep neural networks. Gigascience 2021; 10:giab032. [PMID: 33954794 PMCID: PMC8099770 DOI: 10.1093/gigascience/giab032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 03/31/2021] [Accepted: 04/13/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Fluorescence microscopy is an important technique in many areas of biological research. Two factors that limit the usefulness and performance of fluorescence microscopy are photobleaching of fluorescent probes during imaging and, when imaging live cells, phototoxicity caused by light exposure. Recently developed methods in machine learning are able to greatly improve the signal-to-noise ratio of acquired images. This allows researchers to record images with much shorter exposure times, which in turn minimizes photobleaching and phototoxicity by reducing the dose of light reaching the sample. FINDINGS To use deep learning methods, a large amount of data is needed to train the underlying convolutional neural network. One way to do this involves use of pairs of fluorescence microscopy images acquired with long and short exposure times. We provide high-quality datasets that can be used to train and evaluate deep learning methods under development. CONCLUSION The availability of high-quality data is vital for training convolutional neural networks that are used in current machine learning approaches.
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Affiliation(s)
- Guy M Hagen
- UCCS BioFrontiers Center, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA
| | - Justin Bendesky
- UCCS BioFrontiers Center, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA
| | - Rosa Machado
- UCCS BioFrontiers Center, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA
| | - Tram-Anh Nguyen
- George Mason University, 4400 University Drive, Fairfax, VA 22030, USA
| | - Tanmay Kumar
- Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Jonathan Ventura
- Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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155
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Hardo G, Bakshi S. Challenges of analysing stochastic gene expression in bacteria using single-cell time-lapse experiments. Essays Biochem 2021; 65:67-79. [PMID: 33835126 PMCID: PMC8056041 DOI: 10.1042/ebc20200015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023]
Abstract
Stochastic gene expression causes phenotypic heterogeneity in a population of genetically identical bacterial cells. Such non-genetic heterogeneity can have important consequences for the population fitness, and therefore cells implement regulation strategies to either suppress or exploit such heterogeneity to adapt to their circumstances. By employing time-lapse microscopy of single cells, the fluctuation dynamics of gene expression may be analysed, and their regulatory mechanisms thus deciphered. However, a careful consideration of the experimental design and data-analysis is needed to produce useful data for deriving meaningful insights from them. In the present paper, the individual steps and challenges involved in a time-lapse experiment are discussed, and a rigorous framework for designing, performing, and extracting single-cell gene expression dynamics data from such experiments is outlined.
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Affiliation(s)
- Georgeos Hardo
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Somenath Bakshi
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
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156
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Vasse GF, Buzón P, Melgert BN, Roos WH, van Rijn P. Single Cell Reactomics: Real-Time Single-Cell Activation Kinetics of Optically Trapped Macrophages. SMALL METHODS 2021; 5:e2000849. [PMID: 34927846 DOI: 10.1002/smtd.202000849] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/27/2021] [Indexed: 05/29/2023]
Abstract
Macrophages are well known for their role in immune responses and tissue homeostasis. They can polarize towards various phenotypes in response to biophysical and biochemical stimuli. However, little is known about the early kinetics of macrophage polarization in response to single biophysical or biochemical stimuli. Our approach, combining optical tweezers, confocal fluorescence microscopy, and microfluidics, allows us to isolate single macrophages and follow their immediate responses to a biochemical stimulus in real-time. This strategy enables live-cell imaging at high spatiotemporal resolution and omits surface adhesion and cell-cell contact as biophysical stimuli. The approach is validated by successfully following the early phase of an oxidative stress response of macrophages upon phorbol 12-myristate 13-acetate (PMA) stimulation, allowing detailed analysis of the initial macrophage response upon a single biochemical stimulus within seconds after its application, thereby eliminating delay times introduced by other techniques during the stimulation procedure. Hence, an unprecedented view of the early kinetics of macrophage polarization is provided.
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Affiliation(s)
- Gwenda F Vasse
- Biomedical Engineering Department-FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
- Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - Pedro Buzón
- Moleculaire Biofysica, Zernike Instituut, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
| | - Barbro N Melgert
- Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
| | - Patrick van Rijn
- Biomedical Engineering Department-FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
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157
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Belotti Y, Jokhun DS, Ponnambalam JS, Valerio VLM, Lim CT. Machine learning based approach to pH imaging and classification of single cancer cells. APL Bioeng 2021; 5:016105. [PMID: 33758789 PMCID: PMC7968934 DOI: 10.1063/5.0031615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/03/2021] [Indexed: 12/14/2022] Open
Abstract
The ability to identify different cell populations in a noninvasive manner and without the use of fluorescence labeling remains an important goal in biomedical research. Various techniques have been developed over the last decade, which mainly rely on fluorescent probes or nanoparticles. On the other hand, their applications to single-cell studies have been limited by the lengthy preparation and labeling protocols, as well as issues relating to reproducibility and sensitivity. Furthermore, some of these techniques require the cells to be fixed. Interestingly, it has been shown that different cell types exhibit a unique intracellular environment characterized by specific acidity conditions as a consequence of their distinct functions and metabolism. Here, we leverage a recently developed pH imaging modality and machine learning-based single-cell segmentation and classification to identify different cancer cell lines based on their characteristic intracellular pH. This simple method opens up the potential to perform rapid noninvasive identification of living cancer cells for early cancer diagnosis and further downstream analyses.
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Affiliation(s)
- Y Belotti
- Institute for Health Innovation and Technology, National University of Singapore, 117599 Singapore, Singapore
| | - D S Jokhun
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore, Singapore
| | - J S Ponnambalam
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore, Singapore
| | - V L M Valerio
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore, Singapore
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158
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Mimori-Kiyosue Y. Imaging mitotic processes in three dimensions with lattice light-sheet microscopy. Chromosome Res 2021; 29:37-50. [PMID: 33694045 PMCID: PMC8058003 DOI: 10.1007/s10577-021-09656-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022]
Abstract
There are few technologies that can capture mitotic processes occurring in three-dimensional space with the desired spatiotemporal resolution. Due to such technical limitations, our understanding of mitosis, which has been studied since the early 1880s, is still incomplete with regard to mitotic processes and their regulatory mechanisms at a molecular level. A recently developed high-resolution type of light-sheet microscopy, lattice light-sheet microscopy (LLSM), has achieved unprecedented spatiotemporal resolution scans of intracellular spaces at the whole-cell level. This technology enables experiments that were not possible before (e.g., tracking of growth of every spindle microtubule end and discrimination of individual chromosomes in living cells), thus providing a new avenue for the analysis of mitotic processes. Herein, principles of LLSM technology are introduced, as well as experimental techniques that became possible with LLSM. In addition, issues remaining to be solved for use of this technology in mitosis research, big image data problems, are presented to help guide mitosis research into a new era.
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Affiliation(s)
- Yuko Mimori-Kiyosue
- Laboratory for Molecular and Cellular Dynamics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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159
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160
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Joest EF, Winter C, Wesalo JS, Deiters A, Tampé R. Light-guided intrabodies for on-demand in situ target recognition in human cells. Chem Sci 2021; 12:5787-5795. [PMID: 35342543 PMCID: PMC8872839 DOI: 10.1039/d1sc01331a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 03/22/2021] [Indexed: 01/18/2023] Open
Abstract
Nanobodies are ideal to visualize and modulate targets in living cells. We designed a versatile platform for generating photo-conditional intrabodies by genetic code expansion. After illumination, the intrabodies show fast and stable binding.
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Affiliation(s)
- Eike F. Joest
- Institute of Biochemistry, Biocenter
- Goethe University Frankfurt
- 60438 Frankfurt
- Germany
| | - Christian Winter
- Institute of Biochemistry, Biocenter
- Goethe University Frankfurt
- 60438 Frankfurt
- Germany
| | | | | | - Robert Tampé
- Institute of Biochemistry, Biocenter
- Goethe University Frankfurt
- 60438 Frankfurt
- Germany
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161
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Glenn HL, de Matos AL, Villa N, McFadden G. Microscopic Analysis of Viral Infection. Methods Mol Biol 2021; 2225:163-177. [PMID: 33108662 DOI: 10.1007/978-1-0716-1012-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Viruses engineered to express fluorescent proteins can be used with live-cell imaging techniques to monitor the progression of infection in real time. Here we describe a set of methods to track infection spreading from one cell population to another as well as to visualize transfer of virions between cells. This approach is extended to multiplexing with physiological readouts of cell death, which can be correlated with single-cell resolution to viral infection.
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Affiliation(s)
- Honor L Glenn
- Center for Immunotherapy, Vaccines and Virotherapy, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Ana Lemos de Matos
- Center for Immunotherapy, Vaccines and Virotherapy, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Nancy Villa
- Center for Immunotherapy, Vaccines and Virotherapy, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Grant McFadden
- Center for Immunotherapy, Vaccines and Virotherapy, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
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162
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Schmidt GW, Cuny AP, Rudolf F. Preventing Photomorbidity in Long-Term Multi-color Fluorescence Imaging of Saccharomyces cerevisiae and S. pombe. G3 (BETHESDA, MD.) 2020; 10:4373-4385. [PMID: 33023973 PMCID: PMC7718758 DOI: 10.1534/g3.120.401465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022]
Abstract
Time-lapse imaging of live cells using multiple fluorescent reporters is an essential tool to study molecular processes in single cells. However, exposure to even moderate doses of visible excitation light can disturb cellular physiology and alter the quantitative behavior of the cells under study. Here, we set out to develop guidelines to avoid the confounding effects of excitation light in multi-color long-term imaging. We use widefield fluorescence microscopy to measure the effect of the administered excitation light on growth rate (here called photomorbidity) in yeast. We find that photomorbidity is determined by the cumulative light dose at each wavelength, but independent of the way excitation light is applied. Importantly, photomorbidity possesses a threshold light dose below which no effect is detectable (NOEL). We found, that the suitability of fluorescent proteins for live-cell imaging at the respective excitation light NOEL is equally determined by the cellular autofluorescence and the fluorescent protein brightness. Last, we show that photomorbidity of multiple wavelengths is additive and imaging conditions absent of photomorbidity can be predicted. Our findings enable researchers to find imaging conditions with minimal impact on physiology and can provide framework for how to approach photomorbidity in other organisms.
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Affiliation(s)
- Gregor W Schmidt
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland and
| | - Andreas P Cuny
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland and
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Fabian Rudolf
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland and
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
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163
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Wait EC, Reiche MA, Chew TL. Hypothesis-driven quantitative fluorescence microscopy - the importance of reverse-thinking in experimental design. J Cell Sci 2020; 133:133/21/jcs250027. [PMID: 33154172 DOI: 10.1242/jcs.250027] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
One of the challenges in modern fluorescence microscopy is to reconcile the conventional utilization of microscopes as exploratory instruments with their emerging and rapidly expanding role as a quantitative tools. The contribution of microscopy to observational biology will remain enormous owing to the improvements in acquisition speed, imaging depth, resolution and biocompatibility of modern imaging instruments. However, the use of fluorescence microscopy to facilitate the quantitative measurements necessary to challenge hypotheses is a relatively recent concept, made possible by advanced optics, functional imaging probes and rapidly increasing computational power. We argue here that to fully leverage the rapidly evolving application of microscopes in hypothesis-driven biology, we not only need to ensure that images are acquired quantitatively but must also re-evaluate how microscopy-based experiments are designed. In this Opinion, we present a reverse logic that guides the design of quantitative fluorescence microscopy experiments. This unique approach starts from identifying the results that would quantitatively inform the hypothesis and map the process backward to microscope selection. This ensures that the quantitative aspects of testing the hypothesis remain the central focus of the entire experimental design.
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Affiliation(s)
- Eric C Wait
- Advanced Imaging Center, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Michael A Reiche
- Advanced Imaging Center, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
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164
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BrainPhys neuronal medium optimized for imaging and optogenetics in vitro. Nat Commun 2020; 11:5550. [PMID: 33144563 PMCID: PMC7642238 DOI: 10.1038/s41467-020-19275-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
The capabilities of imaging technologies, fluorescent sensors, and optogenetics tools for cell biology are advancing. In parallel, cellular reprogramming and organoid engineering are expanding the use of human neuronal models in vitro. This creates an increasing need for tissue culture conditions better adapted to live-cell imaging. Here, we identify multiple caveats of traditional media when used for live imaging and functional assays on neuronal cultures (i.e., suboptimal fluorescence signals, phototoxicity, and unphysiological neuronal activity). To overcome these issues, we develop a neuromedium called BrainPhys™ Imaging (BPI) in which we optimize the concentrations of fluorescent and phototoxic compounds. BPI is based on the formulation of the original BrainPhys medium. We benchmark available neuronal media and show that BPI enhances fluorescence signals, reduces phototoxicity and optimally supports the electrical and synaptic activity of neurons in culture. We also show the superior capacity of BPI for optogenetics and calcium imaging of human neurons. Altogether, our study shows that BPI improves the quality of a wide range of fluorescence imaging applications with live neurons in vitro while supporting optimal neuronal viability and function. Current media for neuronal cell and organoid cultures are suboptimal for functional imaging and optogenetics experiments, owing to phototoxicity and unphysiological performance. Here the authors formulate an optimised neuronal medium to support live cell imaging and electrophysiological activity.
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165
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Schmidt E, Oheim M. Infrared Excitation Induces Heating and Calcium Microdomain Hyperactivity in Cortical Astrocytes. Biophys J 2020; 119:2153-2165. [PMID: 33130118 DOI: 10.1016/j.bpj.2020.10.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/01/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022] Open
Abstract
Unraveling how neural networks process and represent sensory information and how these cellular signals instruct behavioral output is a main goal in neuroscience. Two-photon activation of optogenetic actuators and calcium (Ca2+) imaging with genetically encoded indicators allow, respectively, the all-optical stimulation and readout of activity from genetically identified cell populations. However, these techniques locally expose the brain to high near-infrared light doses, raising the concern of light-induced adverse effects on the biology under study. Combining 2P imaging of Ca2+ transients in GCaMP6f-expressing cortical astrocytes and unbiased machine-based event detection, we demonstrate the subtle build-up of aberrant microdomain Ca2+ transients in the fine astroglial processes that depended on the average rather than peak laser power. Illumination conditions routinely being used in biological 2P microscopy (920-nm excitation, ∼100-fs, and ∼10 mW average power) increased the frequency of microdomain Ca2+ events but left their amplitude, area, and duration largely unchanged. Ca2+ transients in the otherwise silent soma were secondary to this peripheral hyperactivity that occurred without overt morphological damage. Continuous-wave (nonpulsed) 920-nm illumination at the same average power was as damaging as femtosecond pulses, unraveling the dominance of a heating-mediated damage mechanism. In an astrocyte-specific inositol 3-phosphate receptor type-2 knockout mouse, near-infrared light-induced Ca2+ microdomains persisted in the small processes, underpinning their resemblance to physiological inositol 3-phosphate receptor type-2-independent Ca2+ signals, whereas somatic hyperactivity was abolished. We conclude that, contrary to what has generally been believed in the field, shorter pulses and lower average power can help to alleviate damage and allow for longer recording windows at 920 nm.
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Affiliation(s)
- Elke Schmidt
- Université de Paris, SPPIN - Saints-Pères Paris Institute for the Neurosciences, CNRS, Paris, France
| | - Martin Oheim
- Université de Paris, SPPIN - Saints-Pères Paris Institute for the Neurosciences, CNRS, Paris, France.
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166
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Zimmermann M, Maia Chagas A, Bartel P, Pop S, Prieto-Godino L, Baden T. LED Zappelin': An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging. HARDWAREX 2020; 8:e00127. [PMID: 35498254 PMCID: PMC9041195 DOI: 10.1016/j.ohx.2020.e00127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 05/19/2023]
Abstract
Two-photon (2P) microscopy is a cornerstone technique in neuroscience research. However, combining 2P imaging with spectrally arbitrary light stimulation can be challenging due to crosstalk between stimulation light and fluorescence detection. To overcome this limitation, we present a simple and low-cost electronic solution based on an ESP32 microcontroller and a TLC5947 LED driver to rapidly time-interleave stimulation and detection epochs during scans. Implemented for less than $100, our design can independently drive up to 24 arbitrary spectrum LEDs to meet user requirements. We demonstrate the utility of our stimulator for colour vision experiments on the in vivo tetrachromatic zebrafish retina and for optogenetic circuit mapping in Drosophila.
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Affiliation(s)
- M.J.Y. Zimmermann
- Sussex Neuroscience, School of Life Sciences, University of Sussex, United Kingdom
| | - A. Maia Chagas
- Sussex Neuroscience, School of Life Sciences, University of Sussex, United Kingdom
- TReND in Africa (www.TReNDinAfrica.org), United Kingdom
- GOSH Community (http://openhardware.science/)
- Institute for Ophthalmic Research, University of Tübingen, Germany
| | - P. Bartel
- Sussex Neuroscience, School of Life Sciences, University of Sussex, United Kingdom
| | - S. Pop
- The Francis Crick Institute, London, United Kingdom
| | - L.L. Prieto-Godino
- TReND in Africa (www.TReNDinAfrica.org), United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - T. Baden
- Sussex Neuroscience, School of Life Sciences, University of Sussex, United Kingdom
- TReND in Africa (www.TReNDinAfrica.org), United Kingdom
- Institute for Ophthalmic Research, University of Tübingen, Germany
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167
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Yu W, Wang S, Cao D, Rui H, Liu C, Sheng Y, Sun Y, Zhang J, Xu J, Jiang D. Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient Variant. iScience 2020; 23:101555. [PMID: 33083724 PMCID: PMC7522124 DOI: 10.1016/j.isci.2020.101555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/24/2020] [Accepted: 09/09/2020] [Indexed: 02/07/2023] Open
Abstract
An oxidative DNA-cleaving DNAzyme (PL) employs a double-cofactor model “X/Cu2+” for catalysis. Herein, we verified that reduced nicotinamide adenine dinucleotide (NADH), flavin mononucleotide, cysteine, dithiothreitol, catechol, resorcinol, hydroquinone, phloroglucinol, o-phenylenediamine, 3,3′,5,5'-tetramethylbenzidine, and hydroxylamine acted as cofactor X. According to their structural similarities or fluorescence property, we further confirmed that reduced nicotinamide adenine dinucleotide phosphate (NADPH), 2-mercaptoethanol, dopamine, chlorogenic acid, resveratrol, and 5-carboxyfluorescein also functioned as cofactor X. Superoxide anions might be the commonality behind these cofactors. We subsequently determined the conservative change of individual nucleotides in the catalytic core under four different cofactor X. The nucleotides A4 and C5 are highly conserved, whereas the conservative levels of other nucleotides are dependent on the types of cofactor X. Moreover, we observed that the minor change in the PL's secondary structure affects electrophoretic mobility. Finally, we characterized a highly efficient variant T3G and converted its double-cofactor NADH/Cu2+ to sole-cofactor NADH. An oxidative cleavage DNAzyme works with various cofactor X Catalytic nucleotide conservation fluctuates with different cofactor X The PL DNAzyme's minor secondary structure change affects electrophoretic mobility Double-cofactor model of the variant T3G can be converted to sole-cofactor model
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Affiliation(s)
- Wenqian Yu
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Shijin Wang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Dongling Cao
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Hongyue Rui
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Chengcheng Liu
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Yongjie Sheng
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Yanhong Sun
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Jin Zhang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Jiacui Xu
- College of Animal Sciences, Jilin University, 5333# Xi'an Road, Changchun 130062, China
- Corresponding author
| | - Dazhi Jiang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
- Corresponding author
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168
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Luo Z, Yurt A, Stahl R, Carlon MS, Ramalho AS, Vermeulen F, Lambrechts A, Braeken D, Lagae L. Fast compressive lens-free tomography for 3D biological cell culture imaging. OPTICS EXPRESS 2020; 28:26935-26952. [PMID: 32906958 DOI: 10.1364/oe.393492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
We present a compressive lens-free technique that performs tomographic imaging across a cubic millimeter-scale volume from highly sparse data. Compared with existing lens-free 3D microscopy systems, our method requires an order of magnitude fewer multi-angle illuminations for tomographic reconstruction, leading to a compact, cost-effective and scanning-free setup with a reduced data acquisition time to enable high-throughput 3D imaging of dynamic biological processes. We apply a fast proximal gradient algorithm with composite regularization to address the ill-posed tomographic inverse problem. Using simulated data, we show that the proposed method can achieve a reconstruction speed ∼10× faster than the state-of-the-art inverse problem approach in 3D lens-free microscopy. We experimentally validate the effectiveness of our method by imaging a resolution test chart and polystyrene beads, demonstrating its capability to resolve micron-size features in both lateral and axial directions. Furthermore, tomographic reconstruction results of neuronspheres and intestinal organoids reveal the potential of this 3D imaging technique for high-resolution and high-throughput biological applications.
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169
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Czechowska K, Lannigan J, Wang L, Arcidiacono J, Ashhurst TM, Barnard RM, Bauer S, Bispo C, Bonilla DL, Brinkman RR, Cabanski M, Chang HD, Chakrabarti L, Chojnowski G, Cotleur B, Degheidy H, Dela Cruz GV, Eck S, Elliott J, Errington R, Filby A, Gagnon D, Gardner R, Green C, Gregory M, Groves CJ, Hall C, Hammes F, Hedrick M, Hoffman R, Icha J, Ivaska J, Jenner DC, Jones D, Kerckhof FM, Kukat C, Lanham D, Leavesley S, Lee M, Lin-Gibson S, Litwin V, Liu Y, Molloy J, Moore JS, Müller S, Nedbal J, Niesner R, Nitta N, Ohlsson-Wilhelm B, Paul NE, Perfetto S, Portat Z, Props R, Radtke S, Rayanki R, Rieger A, Rogers S, Rubbens P, Salomon R, Schiemann M, Sharpe J, Sonder SU, Stewart JJ, Sun Y, Ulrich H, Van Isterdael G, Vitaliti A, van Vreden C, Weber M, Zimmermann J, Vacca G, Wallace P, Tárnok A. Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops. Cytometry A 2020; 95:598-644. [PMID: 31207046 DOI: 10.1002/cyto.a.23777] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Joanne Lannigan
- Flow Cytometry Core, University of Virginia, School of Medicine, 1300 Jefferson Park Ave., Charlottesville, Virginia
| | - Lili Wang
- Biosystems and Biomaterials Division, National Institute of Standards and Technology (NIST), 100 Bureau Drive, Stop 8312, Gaithersburg, Maryland
| | - Judith Arcidiacono
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland
| | - Thomas M Ashhurst
- Sydney Cytometry Facility, Discipline of Pathology, and Ramaciotti Facility for Human Systems Biology; Charles Perkins Centre, The University of Sydney and Centenary Institute, New South Wales, Australia
| | - Ruth M Barnard
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, UK
| | - Steven Bauer
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland
| | - Cláudia Bispo
- UCSF Parnassus Flow Cytometry Core Facility, 513 Parnassus Ave, San Francisco, California
| | - Diana L Bonilla
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ryan R Brinkman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Terry Fox Laboratory, BC Cancer, Vancouver, Canada
| | - Maciej Cabanski
- Novartis Pharma AG, Fabrikstrasse 10-4.27.02, CH-4056, Basel, Switzerland
| | - Hyun-Dong Chang
- Schwiete-Laboratory Microbiota and Inflammation, German Rheumatism Research Centre Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Lina Chakrabarti
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | - Grace Chojnowski
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland 4006, Australia
| | | | - Heba Degheidy
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland
| | - Gelo V Dela Cruz
- Flow Cytometry Platform, Novo Nordisk Center for Stem Cell Biology - Danstem, University of Copenhagen, 3B Blegdamsvej, DK-2200, Copenhagen, Denmark
| | - Steven Eck
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | - John Elliott
- Biosystems and Biomaterials Division, National Institute of Standards and Technology (NIST), 100 Bureau Drive, Stop 8312, Gaithersburg, Maryland
| | | | - Andy Filby
- Newcastle University, Flow Cytometry Core Facility, Newcastle upon Tyne, Tyne and Wear NE1 7RU, UK
| | | | - Rui Gardner
- Memorial Sloan Kettering Cancer Center, Flow Cytometry Core, New York, New York
| | | | - Michael Gregory
- Division of Advanced Research Technologies, New York University Langone Health, New York, New York
| | - Christopher J Groves
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | | | - Frederik Hammes
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | | | - Jaroslav Icha
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Johanna Ivaska
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.,Department of Biochemistry, University of Turku, Turku, Finland
| | - Dominic C Jenner
- Defence Science and Technology Laboratory, Chemical Biological and Radiological Division, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | | | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Köln, Germany
| | | | | | - Michael Lee
- The University California San Francisco, 505 Parnassus Ave, San Francisco, California
| | - Sheng Lin-Gibson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology (NIST), 100 Bureau Drive, Stop 8312, Gaithersburg, Maryland
| | - Virginia Litwin
- Memorial Sloan Kettering Cancer Center, Flow Cytometry Core, New York, New York
| | | | - Jenny Molloy
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | | | - Susann Müller
- Working Group Flow Cytometry, Department of Environmental Microbiology, Helmholtz Center for Environmental Research (UFZ), Leipzig, Germany
| | - Jakub Nedbal
- Marylou Ingram ISAC Scholar, King's College London, UK
| | - Raluca Niesner
- Marylou Ingram ISAC Scholar, German Rheumatism Research Centre, Berlin, Germany
| | - Nao Nitta
- Department of Chemistry, The University of Tokyo
| | - Betsy Ohlsson-Wilhelm
- SciGro, North Central Office, Foster Plaza 5, Suite 300/PMB 20, 651 Holiday Drive, Pittsburgh, Pennsylvania
| | - Nicole E Paul
- LMA CyTOF Core, Dana-Faber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts
| | - Stephen Perfetto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institute of Health (NIH), 40 Convent Drive, Bethesda, Maryland
| | - Ziv Portat
- Weizmann Institute of Science, Life Sciences Core Facilities, Flow Cytometry Unit, Rehovot, 7610001, Israel
| | - Ruben Props
- Center for Microbial Ecology and Technology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Stefan Radtke
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington
| | - Radhika Rayanki
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | - Aja Rieger
- Faculty of Medicine and Dentistry Flow Cytometry Facility, Department of Medical Microbiology & Immunology, University of Alberta, 6-020C Katz Group Centre for Pharmacy and Health Research, Canada
| | - Samson Rogers
- TTP plc, Melbourn Science Park, Melbourn, Hertfordshire SG8 6EE, UK
| | - Peter Rubbens
- KERMIT, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Robert Salomon
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, New South Wales, Australia
| | - Matthias Schiemann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - John Sharpe
- Cytonome/ST LLC, 9 Oak Park Drive, Bedford, Massachusetts
| | | | - Jennifer J Stewart
- Flow Contract Site Laboratory, LLC 18323, Bothell, Everett Highway, Suite 110, Bothell, Washington
| | | | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Gert Van Isterdael
- VIB Flow Core, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, B-9052, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Caryn van Vreden
- Sydney Cytometry Facility and Ramaciotti Facility for Human Systems Biology, The University of Sydney and Centenary Institute, Camperdown, New South Wales 2050, Australia
| | - Michael Weber
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Jacob Zimmermann
- Mucosal Immunology and Host-Microbial Mutualism laboratories, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Paul Wallace
- Roswell Park Comprehensive Cancer Center, New York
| | - Attila Tárnok
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany.,Department Therapy Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
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170
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Li H, Fang J, Wei X, Xu D, Zhang T, Xiang Y, Chen HJ, Liu F, Xie X, Wang P, Hu N. Specific recognition of ion channel blocker by high-content cardiomyocyte electromechanical integrated correlation. Biosens Bioelectron 2020; 162:112273. [DOI: 10.1016/j.bios.2020.112273] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/29/2020] [Accepted: 05/02/2020] [Indexed: 12/22/2022]
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171
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Baumschlager A, Rullan M, Khammash M. Exploiting natural chemical photosensitivity of anhydrotetracycline and tetracycline for dynamic and setpoint chemo-optogenetic control. Nat Commun 2020; 11:3834. [PMID: 32737309 PMCID: PMC7395757 DOI: 10.1038/s41467-020-17677-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 07/02/2020] [Indexed: 01/02/2023] Open
Abstract
The transcriptional inducer anhydrotetracycline (aTc) and the bacteriostatic antibiotic tetracycline (Tc) are commonly used in all fields of biology for control of transcription or translation. A drawback of these and other small molecule inducers is the difficulty of their removal from cell cultures, limiting their application for dynamic control. Here, we describe a simple method to overcome this limitation, and show that the natural photosensitivity of aTc/Tc can be exploited to turn them into highly predictable optogenetic transcriptional- and growth-regulators. This new optogenetic class uniquely features both dynamic and setpoint control which act via population-memory adjustable through opto-chemical modulation. We demonstrate this method by applying it for dynamic gene expression control and for enhancing the performance of an existing optogenetic system. We then expand the utility of the aTc system by constructing a new chemical bandpass filter that increases its aTc response range. The simplicity of our method enables scientists and biotechnologists to use their existing systems employing aTc/Tc for dynamic optogenetic experiments without genetic modification.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Marc Rullan
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
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172
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Le P, Vaidya R, Smith LD, Han Z, Zahid MU, Winter J, Sarkar S, Chung HJ, Perez-Pinera P, Selvin PR, Smith AM. Optimizing Quantum Dot Probe Size for Single-Receptor Imaging. ACS NANO 2020; 14:8343-8358. [PMID: 32525656 PMCID: PMC7872344 DOI: 10.1021/acsnano.0c02390] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Quantum dots (QDs) are nanocrystals with bright fluorescence and long-term photostability, attributes particularly beneficial for single-molecule imaging and molecular counting in the life sciences. The size of a QD nanocrystal determines its physicochemical and photophysical properties, both of which dictate the success of imaging applications. Larger nanocrystals typically have better optical properties, with higher brightness, red-shifted emission, reduced blinking, and greater stability. However, larger nanocrystals introduce molecular-labeling biases due to steric hindrance and nonspecific binding. Here, we systematically analyze the impact of nanocrystal size on receptor labeling in live and fixed cells. We designed three (core)shell QDs with red emission (600-700 nm) and crystalline sizes of 3.2, 5.5, and 8.3 nm. After coating with the same multidentate polymer, hydrodynamic sizes were 9.2 nm (QD9.2), 13.3 nm (QD13.3), and 17.4 nm (QD17.4), respectively. The QDs were conjugated to streptavidin and applied as probes for biotinylated neurotransmitter receptors. QD9.2 exhibited the highest labeling specificity for receptors in the narrow synaptic cleft (∼20-30 nm) in living neurons. However, for dense receptor labeling for molecular counting in live and fixed HeLa cells, QD13.3 yielded the highest counts. Nonspecific binding rose sharply for hydrodynamic sizes larger than 13.3 nm, with QD17.4 exhibiting particularly diminished specificity. Our comparisons further highlight needs to continue engineering the smallest QDs to increase single-molecule intensity, suppress blinking frequency, and inhibit nonspecific labeling in fixed and permeabilized cells. These results lay a foundation for designing QD probes with further reduced sizes to achieve unbiased labeling for quantitative and single-molecule imaging.
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Affiliation(s)
- Phuong Le
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Rohit Vaidya
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lucas D Smith
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zhiyuan Han
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mohammad U Zahid
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jackson Winter
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Suresh Sarkar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee Jung Chung
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, Urbana, Illinois 61801 United States
| | - Paul R Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Departments of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, Urbana, Illinois 61801 United States
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173
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Reimann H, Stopper H, Hintzsche H. Long-term fate of etoposide-induced micronuclei and micronucleated cells in Hela-H2B-GFP cells. Arch Toxicol 2020; 94:3553-3561. [PMID: 32681187 PMCID: PMC7502055 DOI: 10.1007/s00204-020-02840-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]
Abstract
Micronuclei are small nuclear cellular structures containing whole chromosomes or chromosomal fragments. While there is a lot of information available about the origin and formation of micronuclei, less is known about the fate of micronuclei and micronucleated cells. Possible fates include extrusion, degradation, reincorporation and persistence. Live cell imaging was performed to quantitatively analyse the fates of micronuclei and micronucleated cells occurring in vitro. Imaging was conducted for up to 96 h in HeLa-H2B-GFP cells treated with 0.5, 1 and 2 µg/ml etoposide. While a minority of micronuclei was reincorporated into the main nucleus during mitosis, the majority of micronuclei persisted without any alterations. Degradation and extrusion were observed rarely or never. The presence of micronuclei affected the proliferation of the daughter cells and also had an influence on cell death rates. Mitotic errors were found to be clearly increased in micronucleus-containing cells. The results show that micronuclei and micronucleated cells can, although delayed in cell cycle, sustain for multiple divisions.
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Affiliation(s)
- Hauke Reimann
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany
| | - Henning Hintzsche
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany. .,Bavarian Health and Food Safety Authority, Eggenreuther Weg 43, 91058, Erlangen, Germany.
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174
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Rhee JK, Leong LM, Mukim MSI, Kang BE, Lee S, Bilbao-Broch L, Baker BJ. Biophysical Parameters of GEVIs: Considerations for Imaging Voltage. Biophys J 2020; 119:1-8. [PMID: 32521239 PMCID: PMC7335909 DOI: 10.1016/j.bpj.2020.05.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 04/17/2020] [Accepted: 05/20/2020] [Indexed: 11/29/2022] Open
Abstract
Genetically encoded voltage indicators (GEVIs) continue to evolve, resulting in many different probes with varying strengths and weaknesses. Developers of new GEVIs tend to highlight their positive features. A recent article from an independent laboratory has compared the signal/noise ratios of a number of GEVIs. Such a comparison can be helpful to investigators eager to try to image the voltage of excitable cells. In this perspective, we will present examples of how the biophysical features of GEVIs affect the imaging of excitable cells in an effort to assist researchers when considering probes for their specific needs.
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Affiliation(s)
- Jun Kyu Rhee
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Lee Min Leong
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Md Sofequl Islam Mukim
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Bok Eum Kang
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Sungmoo Lee
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Laura Bilbao-Broch
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Bradley J Baker
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea.
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175
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Krejcir R, Briza T, Sterba M, Simoncik O, Muller P, Coates PJ, Martasek P, Vojtesek B, Zatloukalova P. Anticancer pentamethinium salt is a potent photosensitizer inducing mitochondrial disintegration and apoptosis upon red light illumination. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 209:111939. [PMID: 32640366 DOI: 10.1016/j.jphotobiol.2020.111939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/27/2022]
Abstract
Despite progress in the development and application of novel therapeutic agents, cancer remains a major cause of death worldwide. Therefore, there is a need for new approaches to increase therapeutic options and efficiency. The metabolism of cancer cells differs from that of non-malignant cells and their mitochondria show altered activities that can be utilized as a target for drug development. Salt 1 is a low-molecular weight heterocyclic compound of the polymethine class that accumulates in the mitochondria of cancer cells and selectively disrupts their metabolism. Salt 1 leads to a non-apoptotic form of cell death in vitro that is associated with an autophagic cellular response and eventual metabolic collapse, and inhibits human tumor xenograft growth in vivo without apparent toxicity for normal cells. As a pentamethinium compound, salt 1 exhibits intrinsic fluorescence and is a candidate for photosensitization after excitation by appropriate wavelengths of light. Herein, we report that salt 1 is a potent photosensitizer, which generates a photodynamic effect and provides enhanced cytotoxicity compared to salt 1 without light exposure. Importantly, photosensitization is optimally induced by red light, which is used clinically for photosensitization and penetrates further into tissues than lower wavelengths. Cancer cells treated with non-cytotoxic doses of salt 1 and subsequently exposed to 630 nm light show severely damaged mitochondria, manifested by reduced mitochondrial membrane potential and disintegration of the mitochondrial tubular network. As a consequence, cancer cells lose their proliferative potential and die via apoptosis in the presence of light. These findings indicate that salt 1 is a promising photosensitizer with potential to be combined with 630 nm light to strengthen its efficacy in cancer therapy.
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Affiliation(s)
- Radovan Krejcir
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomas Briza
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic; BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Martin Sterba
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Oliver Simoncik
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Petr Muller
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Philip J Coates
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Pavel Martasek
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague, Kateřinská 32, 121 08 Prague 2, Czech Republic; General University Hospital, U nemocnice 2, 128 08 Prague 2, Czech Republic
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic.
| | - Pavlina Zatloukalova
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic.
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176
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Abstract
The light (or optical) microscope is the icon of science. The aphorism "seeing is believing" is often quoted in scientific papers involving microscopy. Unlike many scientific instruments, the light microscope will deliver an image however badly it is set up. Fluorescence microscopy is a widely used research tool across all disciplines of biological and biomedical science. Most universities and research institutions have microscopes, including confocal microscopes. This introductory paper in a series detailing advanced light microscopy techniques explains the foundations of both electron and light microscopy for biologists and life scientists working with the mouse. An explanation is given of how an image is formed. A description is given of how to set up a light microscope, whether it be a brightfield light microscope on the laboratory bench, a widefield fluorescence microscope, or a confocal microscope. These explanations are accompanied by operational protocols. A full explanation on how to set up and adjust a microscope according to the principles of Köhler illumination is given. The importance of Nyquist sampling is discussed. Guidelines are given on how to choose the best microscope to image the particular sample or slide preparation that you are working with. These are the basic principles of microscopy that a researcher must have an understanding of when operating core bioimaging facility instruments, in order to collect high-quality images. © 2020 The Authors. Basic Protocol 1: Setting up Köhler illumination for a brightfield microscope Basic Protocol 2: Aligning the fluorescence bulb and setting up Köhler illumination for a widefield fluorescence microscope Basic Protocol 3: Generic protocol for operating a confocal microscope.
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Affiliation(s)
- Jeremy Sanderson
- Bioimaging Facility Manager, MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
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177
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Antonacci G, Beck T, Bilenca A, Czarske J, Elsayad K, Guck J, Kim K, Krug B, Palombo F, Prevedel R, Scarcelli G. Recent progress and current opinions in Brillouin microscopy for life science applications. Biophys Rev 2020; 12:615-624. [PMID: 32458371 PMCID: PMC7311586 DOI: 10.1007/s12551-020-00701-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 05/07/2020] [Indexed: 12/20/2022] Open
Abstract
Many important biological functions and processes are reflected in cell and tissue mechanical properties such as elasticity and viscosity. However, current techniques used for measuring these properties have major limitations, such as that they can often not measure inside intact cells and/or require physical contact-which cells can react to and change. Brillouin light scattering offers the ability to measure mechanical properties in a non-contact and label-free manner inside of objects with high spatial resolution using light, and hence has emerged as an attractive method during the past decade. This new approach, coined "Brillouin microscopy," which integrates highly interdisciplinary concepts from physics, engineering, and mechanobiology, has led to a vibrant new community that has organized itself via a European funded (COST Action) network. Here we share our current assessment and opinion of the field, as emerged from a recent dedicated workshop. In particular, we discuss the prospects towards improved and more bio-compatible instrumentation, novel strategies to infer more accurate and quantitative mechanical measurements, as well as our current view on the biomechanical interpretation of the Brillouin spectra.
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Affiliation(s)
- Giuseppe Antonacci
- Photonics Research Group, INTEC, Ghent University-imec, 9052, Ghent, Belgium
- Present address: Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133, Milan, Italy
| | - Timon Beck
- Biotechnology Center, TU Dresden, Dresden, Germany
- Max Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Alberto Bilenca
- Biomedical Engineering Department, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Jürgen Czarske
- Laboratory of Measurement and Sensor System Technique, TU Dresden, Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Kareem Elsayad
- Advanced Microscopy, Vienna Biocenter Core Facilities (VBCF), Vienna, Austria.
| | - Jochen Guck
- Biotechnology Center, TU Dresden, Dresden, Germany
- Max Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Kyoohyun Kim
- Biotechnology Center, TU Dresden, Dresden, Germany
- Max Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Benedikt Krug
- Laboratory of Measurement and Sensor System Technique, TU Dresden, Dresden, Germany
| | | | - Robert Prevedel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Giuliano Scarcelli
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
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178
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Opstad IS, Ströhl F, Fantham M, Hockings C, Vanderpoorten O, van Tartwijk FW, Lin JQ, Tinguely JC, Dullo FT, Kaminski-Schierle GS, Ahluwalia BS, Kaminski CF. A waveguide imaging platform for live-cell TIRF imaging of neurons over large fields of view. JOURNAL OF BIOPHOTONICS 2020; 13:e201960222. [PMID: 32067356 DOI: 10.1002/jbio.201960222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
Large fields of view (FOVs) in total internal reflection fluorescence microscopy (TIRFM) via waveguides have been shown to be highly beneficial for single molecule localisation microscopy on fixed cells [1,2] and have also been demonstrated for short-term live-imaging of robust cell types [3-5], but not yet for delicate primary neurons nor over extended periods of time. Here, we present a waveguide-based TIRFM set-up for live-cell imaging of demanding samples. Using the developed microscope, referred to as the ChipScope, we demonstrate successful culturing and imaging of fibroblasts, primary rat hippocampal neurons and axons of Xenopus retinal ganglion cells (RGCs). The high contrast and gentle illumination mode provided by TIRFM coupled with the exceptionally large excitation areas and superior illumination homogeneity offered by photonic waveguides have potential for a wide application span in neuroscience applications.
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Affiliation(s)
- Ida S Opstad
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Florian Ströhl
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Marcus Fantham
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Colin Hockings
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Oliver Vanderpoorten
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | | | - Julie Qiaojin Lin
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Jean-Claude Tinguely
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Firehun T Dullo
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Balpreet S Ahluwalia
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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179
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Abu-Siniyeh A, Al-Zyoud W. Highlights on selected microscopy techniques to study zebrafish developmental biology. Lab Anim Res 2020; 36:12. [PMID: 32346532 PMCID: PMC7178987 DOI: 10.1186/s42826-020-00044-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023] Open
Abstract
Bio-imaging is a tedious task when it concerns exploring cell functions, developmental mechanisms, and other vital processes in vivo. Single-cell resolution is challenging due to different issues such as sample size, the scattering of intact and opaque tissue, pigmentation in untreated animals, the movement of living organs, and maintaining the sample under physiological conditions. These factors might lead researchers to implement microscopy techniques with a suitable animal model to mimic the nature of the living cells. Zebrafish acquired its prestigious reputation in the biomedical research field due to its transparency under advanced microscopes. Therefore, various microscopy techniques, including Multi-Photon, Light-Sheet Microscopy, and Second Harmonic Generation, simplify the discovery of different types of internal functions in zebrafish. In this review, we briefly discuss three recent microscopy techniques that are being utilized because they are non-invasive in investigating developmental events in zebrafish embryo and larvae.
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Affiliation(s)
- Ahmed Abu-Siniyeh
- 1Clinical Laboratory Sciences Department, College of Applied Medical Science, Taif University, Taif, Kingdom of Saudi Arabia
| | - Walid Al-Zyoud
- 2Department of Biomedical Engineering, School of Applied Medical Sciences, German Jordanian University, Amman, Jordan
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180
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Tosheva KL, Yuan Y, Matos Pereira P, Culley S, Henriques R. Between life and death: strategies to reduce phototoxicity in super-resolution microscopy. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2020; 53:163001. [PMID: 33994582 PMCID: PMC8114953 DOI: 10.1088/1361-6463/ab6b95] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/01/2019] [Accepted: 01/14/2020] [Indexed: 05/23/2023]
Abstract
Super-resolution microscopy (SRM) enables non-invasive, molecule-specific imaging of the internal structure and dynamics of cells with sub-diffraction limit spatial resolution. One of its major limitations is the requirement for high-intensity illumination, generating considerable cellular phototoxicity. This factor considerably limits the capacity for live-cell observations, particularly for extended periods of time. Here, we give an overview of new developments in hardware, software and probe chemistry aiming to reduce phototoxicity. Additionally, we discuss how the choice of biological model and sample environment impacts the capacity for live-cell observations.
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Affiliation(s)
- Kalina L Tosheva
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Yue Yuan
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | | | - Siân Culley
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
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181
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Nerger BA, Nelson CM. Engineered extracellular matrices: emerging strategies for decoupling structural and molecular signals that regulate epithelial branching morphogenesis. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2020; 13:103-112. [PMID: 32864528 PMCID: PMC7451493 DOI: 10.1016/j.cobme.2019.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The extracellular matrix (ECM) is a heterogeneous mixture of proteoglycans and fibrous proteins that form the non-cellular component of tissues and organs. During normal development, homeostasis, and disease progression, the ECM provides dynamic structural and molecular signals that influence the form and function of individual cells and multicellular tissues. Here, we review recent developments in the design and fabrication of engineered ECMs and the application of these systems to study the morphogenesis of epithelial tissues. We emphasize emerging techniques for reproducing the structural and molecular complexity of native ECM, and we highlight how these techniques may be used to decouple the different signals that drive epithelial morphogenesis. Engineered models of native ECM will enable further investigation of the dynamic mechanisms by which the microenvironment influences tissue morphogenesis.
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Affiliation(s)
- Bryan A. Nerger
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Celeste M. Nelson
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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182
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High spatiotemporal resolution and low photo-toxicity fluorescence imaging in live cells and in vivo. Biochem Soc Trans 2020; 47:1635-1650. [PMID: 31829403 DOI: 10.1042/bst20190020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022]
Abstract
Taking advantage of high contrast and molecular specificity, fluorescence microscopy has played a critical role in the visualization of subcellular structures and function, enabling unprecedented exploration from cell biology to neuroscience in living animals. To record and quantitatively analyse complex and dynamic biological processes in real time, fluorescence microscopes must be capable of rapid, targeted access deep within samples at high spatial resolutions, using techniques including super-resolution fluorescence microscopy, light sheet fluorescence microscopy, and multiple photon microscopy. In recent years, tremendous breakthroughs have improved the performance of these fluorescence microscopies in spatial resolution, imaging speed, and penetration. Here, we will review recent advancements of these microscopies in terms of the trade-off among spatial resolution, sampling speed and penetration depth and provide a view of their possible applications.
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183
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Kiepas A, Voorand E, Mubaid F, Siegel PM, Brown CM. Optimizing live-cell fluorescence imaging conditions to minimize phototoxicity. J Cell Sci 2020; 133:jcs242834. [PMID: 31988150 DOI: 10.1242/jcs.242834] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/09/2020] [Indexed: 08/31/2023] Open
Abstract
Fluorescence illumination can cause phototoxicity that negatively affects living samples. This study demonstrates that much of the phototoxicity and photobleaching experienced with live-cell fluorescence imaging occurs as a result of 'illumination overhead' (IO). This occurs when a sample is illuminated but fluorescence emission is not being captured by the microscope camera. Several technological advancements have been developed, including fast-switching LED lamps and transistor-transistor logic (TTL) circuits, to diminish phototoxicity caused by IO. These advancements are not standard features on most microscopes and many biologists are unaware of their necessity for live-cell imaging. IO is particularly problematic when imaging rapid processes that require short exposure times. This study presents a workflow to optimize imaging conditions for measuring both slow and dynamic processes while minimizing phototoxicity on any standard microscope. The workflow includes a guide on how to (1) determine the maximum image exposure time for a dynamic process, (2) optimize excitation light intensity and (3) assess cell health with mitochondrial markers.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Alex Kiepas
- Department of Physiology, McGill University, Montreal, Canada, H3G 1Y6
- Goodman Cancer Research Centre, McGill University, Canada, H3G 1A1
| | - Elena Voorand
- Goodman Cancer Research Centre, McGill University, Canada, H3G 1A1
- Department of Biochemistry, McGill University, Montreal, Canada, H3G 1Y6
| | - Firas Mubaid
- Department of Physiology, McGill University, Montreal, Canada, H3G 1Y6
| | - Peter M Siegel
- Goodman Cancer Research Centre, McGill University, Canada, H3G 1A1
- Department of Biochemistry, McGill University, Montreal, Canada, H3G 1Y6
- Department of Medicine, McGill University, Montreal, Canada, H4A 3J1
- Department of Anatomy & Cell Biology, McGill University, Canada, H3G 0B1
| | - Claire M Brown
- Department of Physiology, McGill University, Montreal, Canada, H3G 1Y6
- Department of Anatomy & Cell Biology, McGill University, Canada, H3G 0B1
- Advanced BioImaging Facility (ABIF), McGill University, Montreal, Canada, H3A 0C7
- Cell Information Systems, McGill University, Montreal, Canada, H3G 0B1
- Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM), McGill University, Montreal, Canada, H3G 1Y6
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184
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Mancebo A, DeMars L, Ertsgaard CT, Puchner EM. Precisely calibrated and spatially informed illumination for conventional fluorescence and improved PALM imaging applications. Methods Appl Fluoresc 2020; 8:025004. [PMID: 31995796 DOI: 10.1088/2050-6120/ab716a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Spatial light modulation using cost efficient digital micromirror devices (DMD) is finding broad applications in fluorescence microscopy due to the reduction of phototoxicity and bleaching and the ability to manipulate proteins in optogenetic experiments. However, precise illumination by DMDs and their application to single-molecule localization microscopy (SMLM) remained a challenge because of non-linear distortions between the DMD and camera coordinate systems caused by optical components in the excitation and emission path. Here we develop a fast and easy to implement calibration procedure that determines these distortions and matches the DMD and camera coordinate system with a precision below the optical diffraction limit. As a result, a region from a fluorescence image can be selected with a higher precision for illumination compared to a rigid transformation allowed by manual alignment of the DMD. We first demonstrate the application of our precisely calibrated light modulation by performing a proof of concept fluorescence recovery after photobleaching experiment with the endoplasmic reticulum-localized protein IRE1 fused to GFP in budding yeast (S. cerevisiae). Next, we develop a spatially informed photoactivation approach for SMLM in which only regions of the cell that contain photoactivatable fluorescent proteins are selected for photoactivation. The reduced exposure of the cells to 405 nm light increased the possible imaging time by 44% until phototoxic effects cause a dominant fluorescence background and a change in cell morphology. As a result, the mean number of reliable single-molecule localizations was also significantly increased by 28%. Since the localization precision and the ability for single-molecule tracking is not altered compared to traditional photoactivation of the entire field of view, spatially informed photoactivation significantly improves the quality of SMLM images and single-molecule tracking data. Our precise calibration method therefore lays the foundation for improved SMLM with active feedback photoactivation far beyond the applications in this work.
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Affiliation(s)
- Angel Mancebo
- School of Physics and Astronomy, University of Minnesota, Physics and Nanotechnology, 115 Union St. SE, Minneapolis, MN 55455, United States of America
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185
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Onukwufor JO, Trewin AJ, Baran TM, Almast A, Foster TH, Wojtovich AP. Quantification of reactive oxygen species production by the red fluorescent proteins KillerRed, SuperNova and mCherry. Free Radic Biol Med 2020; 147:1-7. [PMID: 31841676 PMCID: PMC6980788 DOI: 10.1016/j.freeradbiomed.2019.12.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/03/2019] [Accepted: 12/08/2019] [Indexed: 12/12/2022]
Abstract
Fluorescent proteins can generate reactive oxygen species (ROS) upon absorption of photons via type I and II photosensitization mechanisms. The red fluorescent proteins KillerRed and SuperNova are phototoxic proteins engineered to generate ROS and are used in a variety of biological applications. However, their relative quantum yields and rates of ROS production are unclear, which has limited the interpretation of their effects when used in biological systems. We cloned and purified KillerRed, SuperNova, and mCherry - a related red fluorescent protein not typically considered a photosensitizer - and measured the superoxide (O2•-) and singlet oxygen (1O2) quantum yields with irradiation at 561 nm. The formation of the O2•--specific product 2-hydroxyethidium (2-OHE+) was quantified via HPLC separation with fluorescence detection. Relative to a reference photosensitizer, Rose Bengal, the O2•- quantum yield (ΦO2•-) of SuperNova was determined to be 1.5 × 10-3, KillerRed was 0.97 × 10-3, and mCherry 1.2 × 10-3. At an excitation fluence of 916.5 J/cm2 and matched absorption at 561 nm, SuperNova, KillerRed and mCherry made 3.81, 2.38 and 1.65 μM O2•-/min, respectively. Using the probe Singlet Oxygen Sensor Green (SOSG), we ascertained the 1O2 quantum yield (Φ1O2) for SuperNova to be 22.0 × 10-3, KillerRed 7.6 × 10-3, and mCherry 5.7 × 10-3. These photosensitization characteristics of SuperNova, KillerRed and mCherry improve our understanding of fluorescent proteins and are pertinent for refining their use as tools to advance our knowledge of redox biology.
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Affiliation(s)
- John O Onukwufor
- University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, Rochester, NY, 14642, United States
| | - Adam J Trewin
- University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, Rochester, NY, 14642, United States
| | - Timothy M Baran
- University of Rochester Medical Center, Department of Imaging Sciences, Rochester, 14642, United States
| | - Anmol Almast
- University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, Rochester, NY, 14642, United States
| | - Thomas H Foster
- University of Rochester Medical Center, Department of Imaging Sciences, Rochester, 14642, United States
| | - Andrew P Wojtovich
- University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, Rochester, NY, 14642, United States.
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186
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Image quality guided smart rotation improves coverage in microscopy. Nat Commun 2020; 11:150. [PMID: 31919345 PMCID: PMC6952408 DOI: 10.1038/s41467-019-13821-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 11/29/2019] [Indexed: 11/08/2022] Open
Abstract
Fluorescence microscopy is an essential tool for biological discoveries. There is a constant demand for better spatial resolution across a larger field of view. Although strides have been made to improve the theoretical resolution and speed of the optical instruments, in mesoscopic samples, image quality is still largely limited by the optical properties of the sample. In Selective Plane Illumination Microscopy (SPIM), the achievable optical performance is hampered by optical degradations encountered in both the illumination and detection. Multi-view imaging, either through sample rotation or additional optical paths, is a popular strategy to improve sample coverage. In this work, we introduce a smart rotation workflow that utilizes on-the-fly image analysis to identify the optimal light sheet imaging orientations. The smart rotation workflow outperforms the conventional approach without additional hardware and achieves a better sample coverage using the same number of angles or less and thereby reduces data volume and phototoxicity.
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187
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Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
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Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
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188
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Chen YC, Sood C, Francis AC, Melikyan GB, Dickson RM. Facile autofluorescence suppression enabling tracking of single viruses in live cells. J Biol Chem 2019; 294:19111-19118. [PMID: 31694918 DOI: 10.1074/jbc.ra119.010268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/01/2019] [Indexed: 11/06/2022] Open
Abstract
Live cell fluorescence imaging is the method of choice for studying dynamic processes, such as nuclear transport, vesicular trafficking, and virus entry and egress. However, endogenous cellular autofluorescence masks a useful fluorescence signal, limiting the ability to reliably visualize low-abundance fluorescent proteins. Here, we employed synchronously amplified fluorescence image recovery (SAFIRe), which optically alters ground versus photophysical dark state populations within fluorescent proteins to modulate and selectively detect their background-free emission. Using a photoswitchable rsFastLime fluorescent protein combined with a simple illumination and image-processing scheme, we demonstrate the utility of this approach for suppressing undesirable, unmodulatable fluorescence background. Significantly, we adapted this technique to different commercial wide-field and spinning-disk confocal microscopes, obtaining >10-fold improvements in signal to background. SAFIRe allowed visualization of rsFastLime targeted to mitochondria by efficiently suppressing endogenous autofluorescence or overexpressed cytosolic unmodulatable EGFP. Suppression of the overlapping EGFP signal provided a means to perform multiplexed imaging of rsFastLime and spectrally overlapping fluorophores. Importantly, we used SAFIRe to reliably visualize and track single rsFastLime-labeled HIV-1 particles in living cells exhibiting high and uneven autofluorescence signals. Time-lapse SAFIRe imaging can be performed for an extended period of time to visualize HIV-1 entry into cells. SAFIRe should be broadly applicable for imaging live cell dynamics with commercial microscopes, even in strongly autofluorescent cells or cells expressing spectrally overlapping fluorescent proteins.
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Affiliation(s)
- Yen-Cheng Chen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400.,Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322
| | - Chetan Sood
- Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322
| | - Ashwanth C Francis
- Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322
| | - Gregory B Melikyan
- Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322 .,Children's Healthcare of Atlanta, Atlanta, Georgia 30332
| | - Robert M Dickson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
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189
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Quantification of the morphological characteristics of hESC colonies. Sci Rep 2019; 9:17569. [PMID: 31772193 PMCID: PMC6879623 DOI: 10.1038/s41598-019-53719-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/04/2019] [Indexed: 11/25/2022] Open
Abstract
The maintenance of the undifferentiated state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells and colonies for propagation is typically performed by eye, in terms of the displayed morphological features, such as prominent/abundant nucleoli and a colony with a tightly packed appearance and a well-defined edge. Using image analysis and computational tools, we precisely quantify these properties using phase-contrast images of hESC colonies of different sizes (0.1–1.1 \documentclass[12pt]{minimal}
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\begin{document}$${{\bf{\text{mm}}}}^{{\bf{2}}}$$\end{document}mm2) during days 2, 3 and 4 after plating. Our analyses reveal noticeable differences in their structure influenced directly by the colony area \documentclass[12pt]{minimal}
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\begin{document}$${\boldsymbol{A}}$$\end{document}A. Large colonies (A > 0.6 mm2) have cells with smaller nuclei and a short intercellular distance when compared with small colonies (A < 0.2 mm2). The gaps between the cells, which are present in small and medium sized colonies with A ≤ 0.6 mm2, disappear in large colonies (A > 0.6 mm2) due to the proliferation of the cells in the bulk. This increases the colony density and the number of nearest neighbours. We also detect the self-organisation of cells in the colonies where newly divided (smallest) cells cluster together in patches, separated from larger cells at the final stages of the cell cycle. This might influence directly cell-to-cell interactions and the community effects within the colonies since the segregation induced by size differences allows the interchange of neighbours as the cells proliferate and the colony grows. Our findings are relevant to efforts to determine the quality of hESC colonies and establish colony characteristics database.
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190
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Adaptive prospective optical gating enables day-long 3D time-lapse imaging of the beating embryonic zebrafish heart. Nat Commun 2019; 10:5173. [PMID: 31729395 PMCID: PMC6858381 DOI: 10.1038/s41467-019-13112-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/15/2019] [Indexed: 12/24/2022] Open
Abstract
Three-dimensional fluorescence time-lapse imaging of the beating heart is extremely challenging, due to the heart’s constant motion and a need to avoid pharmacological or phototoxic damage. Although real-time triggered imaging can computationally “freeze” the heart for 3D imaging, no previous algorithm has been able to maintain phase-lock across developmental timescales. We report a new algorithm capable of maintaining day-long phase-lock, permitting routine acquisition of synchronised 3D + time video time-lapse datasets of the beating zebrafish heart. This approach has enabled us for the first time to directly observe detailed developmental and cellular processes in the beating heart, revealing the dynamics of the immune response to injury and witnessing intriguing proliferative events that challenge the established literature on cardiac trabeculation. Our approach opens up exciting new opportunities for direct time-lapse imaging studies over a 24-hour time course, to understand the cellular mechanisms underlying cardiac development, repair and regeneration. Imaging heart development is challenging due to constant tissue movement and changing physical landmarks. Here the authors present an algorithm capable of maintaining phase-locked imaging throughout a 24 hour timespan, enabling long term timelapse imaging studies of zebrafish heart development, repair and regeneration.
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191
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Ticli G, Prosperi E. In Situ Analysis of DNA-Protein Complex Formation upon Radiation-Induced DNA Damage. Int J Mol Sci 2019; 20:ijms20225736. [PMID: 31731696 PMCID: PMC6888283 DOI: 10.3390/ijms20225736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 01/05/2023] Open
Abstract
The importance of determining at the cellular level the formation of DNA–protein complexes after radiation-induced lesions to DNA is outlined by the evidence that such interactions represent one of the first steps of the cellular response to DNA damage. These complexes are formed through recruitment at the sites of the lesion, of proteins deputed to signal the presence of DNA damage, and of DNA repair factors necessary to remove it. Investigating the formation of such complexes has provided, and will probably continue to, relevant information about molecular mechanisms and spatiotemporal dynamics of the processes that constitute the first barrier of cell defense against genome instability and related diseases. In this review, we will summarize and discuss the use of in situ procedures to detect the formation of DNA-protein complexes after radiation-induced DNA damage. This type of analysis provides important information on the spatial localization and temporal resolution of the formation of such complexes, at the single-cell level, allowing the study of heterogeneous cell populations.
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Affiliation(s)
- Giulio Ticli
- Istituto di Genetica Molecolare “Luca Cavalli Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy;
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27100 Pavia, Italy
| | - Ennio Prosperi
- Istituto di Genetica Molecolare “Luca Cavalli Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy;
- Correspondence:
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192
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Al-Gubory KH. Shedding light on fibered confocal fluorescence microscopy: Applications in biomedical imaging and therapies. JOURNAL OF BIOPHOTONICS 2019; 12:e201900146. [PMID: 31343844 DOI: 10.1002/jbio.201900146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/20/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
Discoveries of major importance in life sciences and preclinical research are linked to the invention of microscopes that enable imaging of cells and their microstructures. Imaging technologies involving in vivo procedures using fluorescent dyes that permit labelling of cells have been developed over the last two decades. Fibered confocal fluorescence microscopy (FCFM) is an imaging technology equipped with fiber-optic probes to deliver light to organs and tissues of live animals. This enables not only in vivo detection of fluorescent signals and visualization of cells, but also the study of dynamic processes, such cell proliferation, apoptosis and angiogenesis, under physiological and pathological conditions. This will allow the diagnosis of diseased organs and tissues and the evaluation of the efficacy of new therapies in animal models of human diseases. The aim of this report is to shed light on FCFM and its potential medical applications and discusses some factors that compromise the reliability and reproducibility of monitoring biological processes by FCFM. This report also highlights the issues concerning animal experimentation and welfare, and the contributions of FCFM to the 3Rs principals, replacement, reduction and refinement.
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Affiliation(s)
- Kaïs H Al-Gubory
- National Institute for Agricultural Research, Department of Animal Physiology, Jouy-en-Josas, France
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193
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Live cell imaging of signaling and metabolic activities. Pharmacol Ther 2019; 202:98-119. [DOI: 10.1016/j.pharmthera.2019.06.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/31/2019] [Indexed: 12/15/2022]
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194
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Sachse M, Fernández de Castro I, Tenorio R, Risco C. The viral replication organelles within cells studied by electron microscopy. Adv Virus Res 2019; 105:1-33. [PMID: 31522702 PMCID: PMC7112055 DOI: 10.1016/bs.aivir.2019.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transmission electron microscopy (TEM) has been crucial to study viral infections. As a result of recent advances in light and electron microscopy, we are starting to be aware of the variety of structures that viruses assemble inside cells. Viruses often remodel cellular compartments to build their replication factories. Remarkably, viruses are also able to induce new membranes and new organelles. Here we revise the most relevant imaging technologies to study the biogenesis of viral replication organelles. Live cell microscopy, correlative light and electron microscopy, cryo-TEM, and three-dimensional imaging methods are unveiling how viruses manipulate cell organization. In particular, methods for molecular mapping in situ in two and three dimensions are revealing how macromolecular complexes build functional replication complexes inside infected cells. The combination of all these imaging approaches is uncovering the viral life cycle events with a detail never seen before.
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Affiliation(s)
- Martin Sachse
- Unité Technologie et service BioImagerie Ultrastructurale, Institut Pasteur, Paris, France.
| | | | - Raquel Tenorio
- Cell Structure Laboratory, National Center for Biotechnology, CSIC, Madrid, Spain
| | - Cristina Risco
- Cell Structure Laboratory, National Center for Biotechnology, CSIC, Madrid, Spain.
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195
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Yanakieva I, Erzberger A, Matejčić M, Modes CD, Norden C. Cell and tissue morphology determine actin-dependent nuclear migration mechanisms in neuroepithelia. J Cell Biol 2019; 218:3272-3289. [PMID: 31420451 PMCID: PMC6781452 DOI: 10.1083/jcb.201901077] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/29/2019] [Accepted: 07/18/2019] [Indexed: 11/22/2022] Open
Abstract
Using quantitative live imaging in the developing zebrafish embryo, Yanakieva et al. show that distinct actin-dependent mechanisms position nuclei in neuroepithelia of different morphology. In curved neuroepithelia, a novel formin-dependent mechanism is discovered for which the authors propose a proof-of-principle theoretical model. Correct nuclear position is crucial for cellular function and tissue development. Depending on cell context, however, the cytoskeletal elements responsible for nuclear positioning vary. While these cytoskeletal mechanisms have been intensely studied in single cells, how nuclear positioning is linked to tissue morphology is less clear. Here, we compare apical nuclear positioning in zebrafish neuroepithelia. We find that kinetics and actin-dependent mechanisms of nuclear positioning vary in tissues of different morphology. In straight neuroepithelia, nuclear positioning is controlled by Rho-ROCK–dependent myosin contractility. In contrast, in basally constricted neuroepithelia, a novel formin-dependent pushing mechanism is found for which we propose a proof-of-principle force generation theory. Overall, our data suggest that correct nuclear positioning is ensured by the adaptability of the cytoskeleton to cell and tissue shape. This in turn leads to robust epithelial maturation across geometries. The conclusion that different nuclear positioning mechanisms are favored in tissues of different morphology highlights the importance of developmental context for the execution of intracellular processes.
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Affiliation(s)
- Iskra Yanakieva
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Anna Erzberger
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Marija Matejčić
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Carl D Modes
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Center for Systems Biology, Dresden, Germany
| | - Caren Norden
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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196
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Xu Q, Dong X. Calcium imaging approaches in investigation of pain mechanism in the spinal cord. Exp Neurol 2019; 317:129-132. [PMID: 30853387 PMCID: PMC6544469 DOI: 10.1016/j.expneurol.2019.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/16/2019] [Accepted: 03/06/2019] [Indexed: 11/28/2022]
Abstract
The continuous advancement of microscopic imaging techniques combined with the discovery and use of more powerful calcium indicators has made calcium imaging technology much more effective and has increased its use in the study of pain circuitry. Using calcium imaging to study spinal pain mechanisms causes less damage to animals compared to electrophysiological techniques and is also able to observe the firing pattern of spinal neurons and the connections between them on a large scale. These advantages allow any changes in spinal cord circuits caused by pain transmission to be observed more effectively. This review will discuss the development of calcium indicators over the past decades as well as the various applications of calcium imaging, from in vitro to in vivo spinal cord experiments, in the study of pain circuits. We will also discuss possible directions for the study of spinal pain circuits in the future.
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Affiliation(s)
- Qian Xu
- The Solomon H. Snyder Department of Neuroscience and the Center for Sensory Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience and the Center for Sensory Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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197
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Gorelashvili MG, Angay O, Hemmen K, Klaus V, Stegner D, Heinze KG. Megakaryocyte volume modulates bone marrow niche properties and cell migration dynamics. Haematologica 2019; 105:895-904. [PMID: 31248970 PMCID: PMC7109717 DOI: 10.3324/haematol.2018.202010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 06/25/2019] [Indexed: 12/17/2022] Open
Abstract
All hematopoietic cells that develop in the bone marrow must cross the endothelial barrier to enter the blood circulation. Blood platelets, however, are released by bigger protrusions of huge progenitor cells, named megakaryocytes, and enter the blood stream as so-called proplatelets before fragmenting into mature platelets. Recently, a second function of megakaryocytes has been identified, as they modulate the quiescence of hematopoietic stem cells, mostly via different soluble factors. We know from light sheet fluorescence microscopy images that megakaryocytes are distributed throughout the bone marrow facing a dense vascular network. Here, we used such three-dimensional images to provide a realistic simulation template reflecting the in vivo cell-vessel distributions resulting in reliable whole-bone analysis in silico Combining this approach with an automated image analysis pipeline, we found that megakaryocytes influence migration of neutrophils and hematopoietic stem cells, and thus act as biomechanical restrainers modulating cell mobility and extravasation. Indeed, as a consequence of increased megakaryocyte volumes in platelet-depleted mice neutrophil mobility was reduced in these animals.
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Affiliation(s)
| | - Oğuzhan Angay
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Katherina Hemmen
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Vanessa Klaus
- Institute of Experimental Biomedicine, University Hospital Würzburg
| | - David Stegner
- Institute of Experimental Biomedicine, University Hospital Würzburg .,Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Katrin G Heinze
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
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198
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Scodellaro R, Bouzin M, Mingozzi F, D'Alfonso L, Granucci F, Collini M, Chirico G, Sironi L. Whole-Section Tumor Micro-Architecture Analysis by a Two-Dimensional Phasor-Based Approach Applied to Polarization-Dependent Second Harmonic Imaging. Front Oncol 2019; 9:527. [PMID: 31275857 PMCID: PMC6593899 DOI: 10.3389/fonc.2019.00527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/30/2019] [Indexed: 11/17/2022] Open
Abstract
Second Harmonic Generation (SHG) microscopy has gained much interest in the histopathology field since it allows label-free imaging of tissues simultaneously providing information on their morphology and on the collagen microarchitecture, thereby highlighting the onset of pathologies and diseases. A wide request of image analysis tools is growing, with the aim to increase the reliability of the analysis of the huge amount of acquired data and to assist pathologists in a user-independent way during their diagnosis. In this light, we exploit here a set of phasor-parameters that, coupled to a 2-dimensional phasor-based approach (μMAPPS, Microscopic Multiparametric Analysis by Phasor projection of Polarization-dependent SHG signal) and a clustering algorithm, allow to automatically recover different collagen microarchitectures in the tissues extracellular matrix. The collagen fibrils microscopic parameters (orientation and anisotropy) are analyzed at a mesoscopic level by quantifying their local spatial heterogeneity in histopathology sections (few mm in size) from two cancer xenografts in mice, in order to maximally discriminate different collagen organizations, allowing in this case to identify the tumor area with respect to the surrounding skin tissue. We show that the “fibril entropy” parameter, which describes the tissue order on a selected spatial scale, is the most effective in enlightening the tumor edges, opening the possibility of their automatic segmentation. Our method, therefore, combined with tissue morphology information, has the potential to become a support to standard histopathology in diseases diagnosis.
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Affiliation(s)
| | - Margaux Bouzin
- Physics Department, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Francesca Mingozzi
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Laura D'Alfonso
- Physics Department, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Francesca Granucci
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Maddalena Collini
- Physics Department, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Giuseppe Chirico
- Physics Department, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Laura Sironi
- Physics Department, Università degli Studi di Milano-Bicocca, Milan, Italy
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199
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Pijuan J, Barceló C, Moreno DF, Maiques O, Sisó P, Marti RM, Macià A, Panosa A. In vitro Cell Migration, Invasion, and Adhesion Assays: From Cell Imaging to Data Analysis. Front Cell Dev Biol 2019; 7:107. [PMID: 31259172 PMCID: PMC6587234 DOI: 10.3389/fcell.2019.00107] [Citation(s) in RCA: 286] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/29/2019] [Indexed: 01/08/2023] Open
Abstract
Cell migration is a key procedure involved in many biological processes including embryological development, tissue formation, immune defense or inflammation, and cancer progression. How physical, chemical, and molecular aspects can affect cell motility is a challenge to understand migratory cells behavior. In vitro assays are excellent approaches to extrapolate to in vivo situations and study live cells behavior. Here we present four in vitro protocols that describe step-by-step cell migration, invasion and adhesion strategies and their corresponding image data quantification. These current protocols are based on two-dimensional wound healing assays (comparing traditional pipette tip-scratch assay vs. culture insert assay), 2D individual cell-tracking experiments by live cell imaging and three-dimensional spreading and transwell assays. All together, they cover different phenotypes and hallmarks of cell motility and adhesion, providing orthogonal information that can be used either individually or collectively in many different experimental setups. These optimized protocols will facilitate physiological and cellular characterization of these processes, which may be used for fast screening of specific therapeutic cancer drugs for migratory function, novel strategies in cancer diagnosis, and for assaying new molecules involved in adhesion and invasion metastatic properties of cancer cells.
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Affiliation(s)
- Jordi Pijuan
- Flow Cytometry and Confocal Microscopy Unit, IRBLleida, University of Lleida, Lleida, Spain
| | | | - David F Moreno
- Molecular Biology Institute of Barcelona, CSIC, Barcelona, Spain
| | | | - Pol Sisó
- IRBLleida, University of Lleida, Lleida, Spain
| | - Rosa M Marti
- Department of Dermatology, Hospital Universitari Arnau de Vilanova, University of Lleida, IRBLleida, Lleida, Spain.,Center of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Anna Macià
- IRBLleida, University of Lleida, Lleida, Spain
| | - Anaïs Panosa
- Flow Cytometry and Confocal Microscopy Unit, IRBLleida, University of Lleida, Lleida, Spain
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200
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Abstract
Over the past two decades there have been unprecedented advances in the capabilities for live cell imaging using light and confocal microscopy. Together with the discovery of green fluorescent protein and its derivatives and the development of a vast array of fluorescent imaging probes and conjugates, it is now possible to image virtually any intracellular or extracellular protein or structure. Traditional static imaging of fixed bone cells and tissues takes a snapshot view of events at a specific time point, but can often miss the dynamic aspects of the events being investigated. This chapter provides an overview of the application of live cell imaging approaches for the study of bone cells and bone organ cultures. Rather than emphasizing technical aspects of the imaging equipment, which may vary in different laboratories, we focus on what we consider to be the important principles that are of most practical use for an investigator setting up these techniques in their own laboratory. We also provide detailed protocols that our laboratory has used for live imaging of bone cell and organ cultures.
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Affiliation(s)
- Sarah L Dallas
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri, Kansas City, Kansas City, MO, USA.
| | - Patricia A Veno
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri, Kansas City, Kansas City, MO, USA
| | - LeAnn M Tiede-Lewis
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri, Kansas City, Kansas City, MO, USA
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