101
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Tay NES, Lehnherr D, Rovis T. Photons or Electrons? A Critical Comparison of Electrochemistry and Photoredox Catalysis for Organic Synthesis. Chem Rev 2022; 122:2487-2649. [PMID: 34751568 PMCID: PMC10021920 DOI: 10.1021/acs.chemrev.1c00384] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Redox processes are at the heart of synthetic methods that rely on either electrochemistry or photoredox catalysis, but how do electrochemistry and photoredox catalysis compare? Both approaches provide access to high energy intermediates (e.g., radicals) that enable bond formations not constrained by the rules of ionic or 2 electron (e) mechanisms. Instead, they enable 1e mechanisms capable of bypassing electronic or steric limitations and protecting group requirements, thus enabling synthetic chemists to disconnect molecules in new and different ways. However, while providing access to similar intermediates, electrochemistry and photoredox catalysis differ in several physical chemistry principles. Understanding those differences can be key to designing new transformations and forging new bond disconnections. This review aims to highlight these differences and similarities between electrochemistry and photoredox catalysis by comparing their underlying physical chemistry principles and describing their impact on electrochemical and photochemical methods.
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Affiliation(s)
- Nicholas E S Tay
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Dan Lehnherr
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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102
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Kratz J, Geisler C, Egner A. ISM-assisted tomographic STED microscopy. OPTICS EXPRESS 2022; 30:939-956. [PMID: 35209272 DOI: 10.1364/oe.445441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Stimulated emission depletion (STED) microscopy theoretically provides unlimited resolution. However, in practice the achievable resolution in biological samples is essentially limited by photobleaching. One method which overcomes this problem is tomographic STED (tomoSTED) microscopy. In tomoSTED microscopy, one-dimensional depletion patterns facing in different directions are successively applied in order to acquire a highly-resolved image in two dimensions. In this context, the number of addressed directions depends on the desired angular homogeneity of the point spread function or the optical transfer function and thus on the resolution increase as compared to diffraction-limited imaging. At a reasonable angular homogeneity the light dose and thus bleaching can be reduced, as compared to conventional STED microscopy. Here, we propose and demonstrate for the first time, to our knowledge, that the number of required depletion pattern orientations can be reduced by combining tomoSTED microscopy with the concept of image scanning microscopy (ISM). With our realization of an ISM-tomoSTED microscope, we show that approximately a factor of 2 lower number of orientations are required to achieve the same resolution and image quality as in tomoSTED microscopy.
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103
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Mukherjee S, Thomas C, Wilson R, Simmerman E, Hung ST, Jimenez R. Characterizing Dark State Kinetics and Single Molecule Fluorescence of FusionRed and FusionRed-MQ at Low Irradiances. Phys Chem Chem Phys 2022; 24:14310-14323. [DOI: 10.1039/d2cp00889k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of dark states causes fluorescence intermittency of single molecules due to transitions between “on” and “off” states. Genetically encodable markers such as fluorescent proteins (FPs) exhibit dark states...
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104
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Luo X, Liu J. Ultrasmall Luminescent Metal Nanoparticles: Surface Engineering Strategies for Biological Targeting and Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103971. [PMID: 34796699 PMCID: PMC8787435 DOI: 10.1002/advs.202103971] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/27/2021] [Indexed: 05/07/2023]
Abstract
In the past decade, ultrasmall luminescent metal nanoparticles (ULMNPs, d < 3 nm) have achieved rapid progress in addressing many challenges in the healthcare field because of their excellent physicochemical properties and biological behaviors. With the sharp shrinking size of large plasmonic metal nanoparticles (PMNPs), the contributions from the surface characteristics increase significantly, which brings both opportunities and challenges in the application-driven surface engineering of ULMNPs toward advanced biological applications. Here, the systematic advancements in the biological applications of ULMNPs from bioimaging to theranostics are summarized with emphasis on the versatile surface engineering strategies in the regulation of biological targeting and imaging performance. The efforts in the surface functionalization strategies of ULMNPs for enhanced disease targeting abilities are first discussed. Thereafter, self-assembly strategies of ULMNPs for fabricating multifunctional nanostructures for multimodal imaging and nanomedicine are discussed. Further, surface engineering strategies of ratiometric ULMNPs to enhance the imaging stability to address the imaging challenges in complicated bioenvironments are summarized. Finally, the phototoxicity of ULMNPs and future perspectives are also reviewed, which are expected to provide a fundamental understanding of the physicochemical properties and biological behaviors of ULMNPs to accelerate their future clinical applications in healthcare.
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Affiliation(s)
- Xiaoxi Luo
- Key Laboratory of Functional Molecular Engineering of Guangdong ProvinceSchool of Chemistry and Chemical EngineeringSouth China University of TechnologyGuangzhou510640China
| | - Jinbin Liu
- Key Laboratory of Functional Molecular Engineering of Guangdong ProvinceSchool of Chemistry and Chemical EngineeringSouth China University of TechnologyGuangzhou510640China
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105
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Abstract
Induced pluripotent stem cell (iPSC)-derived organoids provide models to study human organ development. Single-cell transcriptomics enable highly resolved descriptions of cell states within these systems; however, approaches are needed to directly measure lineage relationships. Here we establish iTracer, a lineage recorder that combines reporter barcodes with inducible CRISPR-Cas9 scarring and is compatible with single-cell and spatial transcriptomics. We apply iTracer to explore clonality and lineage dynamics during cerebral organoid development and identify a time window of fate restriction as well as variation in neurogenic dynamics between progenitor neuron families. We also establish long-term four-dimensional light-sheet microscopy for spatial lineage recording in cerebral organoids and confirm regional clonality in the developing neuroepithelium. We incorporate gene perturbation (iTracer-perturb) and assess the effect of mosaic TSC2 mutations on cerebral organoid development. Our data shed light on how lineages and fates are established during cerebral organoid formation. More broadly, our techniques can be adapted in any iPSC-derived culture system to dissect lineage alterations during normal or perturbed development.
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106
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Alghamdi RA, Exposito-Rodriguez M, Mullineaux PM, Brooke GN, Laissue PP. Assessing Phototoxicity in a Mammalian Cell Line: How Low Levels of Blue Light Affect Motility in PC3 Cells. Front Cell Dev Biol 2021; 9:738786. [PMID: 34977004 PMCID: PMC8718804 DOI: 10.3389/fcell.2021.738786] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022] Open
Abstract
Phototoxicity is a significant constraint for live cell fluorescence microscopy. Excessive excitation light intensities change the homeostasis of the observed cells. Erroneous and misleading conclusions may be the problematic consequence of observing such light-induced pathophysiology. In this study, we assess the effect of blue light, as commonly used for GFP and YFP excitation, on a motile mammalian cell line. Tracking PC3 cells at different light doses and intensities, we show how motility can be used to reliably assess subtle positive and negative effects of illumination. We further show that the effects are a factor of intensity rather than light dose. Mitotic delay was not a sensitive indicator of phototoxicity. For early detection of the effect of blue light, we analysed the expression of genes involved in oxidative stress. This study addresses the need for relatively simple and sensitive methods to establish a dose-response curve for phototoxicity in mammalian cell line models. We conclude with a working model for phototoxicity and recommendations for its assessment.
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Affiliation(s)
- Rana A. Alghamdi
- Department of Chemistry, Science and Arts College, Rabigh Campus, King Abdulaziz University, Jeddah, Saudi Arabia
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Marino Exposito-Rodriguez
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | | | - Greg N. Brooke
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Philippe P. Laissue
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- *Correspondence: Philippe P. Laissue,
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107
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Talone B, Bazzarelli M, Schirato A, Dello Vicario F, Viola D, Jacchetti E, Bregonzio M, Raimondi MT, Cerullo G, Polli D. Phototoxicity induced in living HeLa cells by focused femtosecond laser pulses: a data-driven approach. BIOMEDICAL OPTICS EXPRESS 2021; 12:7886-7905. [PMID: 35003873 PMCID: PMC8713694 DOI: 10.1364/boe.441225] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
Nonlinear optical microscopy is a powerful label-free imaging technology, providing biochemical and structural information in living cells and tissues. A possible drawback is photodamage induced by high-power ultrashort laser pulses. Here we present an experimental study on thousands of HeLa cells, to characterize the damage induced by focused femtosecond near-infrared laser pulses as a function of laser power, scanning speed and exposure time, in both wide-field and point-scanning illumination configurations. Our data-driven approach offers an interpretation of the underlying damage mechanisms and provides a predictive model that estimates its probability and extension and a safety limit for the working conditions in nonlinear optical microscopy. In particular, we demonstrate that cells can withstand high temperatures for a short amount of time, while they die if exposed for longer times to mild temperatures. It is thus better to illuminate the samples with high irradiances: thanks to the nonlinear imaging mechanism, much stronger signals will be generated, enabling fast imaging and thus avoiding sample photodamage.
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Affiliation(s)
- B. Talone
- Department of Physics, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | | | - A. Schirato
- Department of Physics, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
- Istituto Italiano di Tecnologia, via Morego 30, I- 16163, Genoa, Italy
| | | | - D. Viola
- Department of Physics, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | - E. Jacchetti
- Department of Chemistry, Materials and Chemical Engineering ’G. Natta’, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | - M. Bregonzio
- 3rdPlace SRL, Foro Bonaparte 71, 20121 Milan, Italy
| | - M. T. Raimondi
- Department of Chemistry, Materials and Chemical Engineering ’G. Natta’, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | - G. Cerullo
- Department of Physics, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
- Istituto di Fotonica e Nanotecnologie (IFN), Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - D. Polli
- Department of Physics, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
- Istituto di Fotonica e Nanotecnologie (IFN), Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
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108
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Wu Y, Han X, Su Y, Glidewell M, Daniels JS, Liu J, Sengupta T, Rey-Suarez I, Fischer R, Patel A, Combs C, Sun J, Wu X, Christensen R, Smith C, Bao L, Sun Y, Duncan LH, Chen J, Pommier Y, Shi YB, Murphy E, Roy S, Upadhyaya A, Colón-Ramos D, La Riviere P, Shroff H. Multiview confocal super-resolution microscopy. Nature 2021; 600:279-284. [PMID: 34837071 PMCID: PMC8686173 DOI: 10.1038/s41586-021-04110-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/07/2021] [Indexed: 12/31/2022]
Abstract
Confocal microscopy1 remains a major workhorse in biomedical optical microscopy owing to its reliability and flexibility in imaging various samples, but suffers from substantial point spread function anisotropy, diffraction-limited resolution, depth-dependent degradation in scattering samples and volumetric bleaching2. Here we address these problems, enhancing confocal microscopy performance from the sub-micrometre to millimetre spatial scale and the millisecond to hour temporal scale, improving both lateral and axial resolution more than twofold while simultaneously reducing phototoxicity. We achieve these gains using an integrated, four-pronged approach: (1) developing compact line scanners that enable sensitive, rapid, diffraction-limited imaging over large areas; (2) combining line-scanning with multiview imaging, developing reconstruction algorithms that improve resolution isotropy and recover signal otherwise lost to scattering; (3) adapting techniques from structured illumination microscopy, achieving super-resolution imaging in densely labelled, thick samples; (4) synergizing deep learning with these advances, further improving imaging speed, resolution and duration. We demonstrate these capabilities on more than 20 distinct fixed and live samples, including protein distributions in single cells; nuclei and developing neurons in Caenorhabditis elegans embryos, larvae and adults; myoblasts in imaginal disks of Drosophila wings; and mouse renal, oesophageal, cardiac and brain tissues.
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Affiliation(s)
- Yicong Wu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
| | - Xiaofei Han
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Department of Automation, Tsinghua University, Beijing, China
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Leica Microsystems, Buffalo Grove, IL, USA
- SVision, Bellevue, WA, USA
| | | | | | - Jiamin Liu
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Titas Sengupta
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Ivan Rey-Suarez
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Robert Fischer
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Akshay Patel
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Christian Combs
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, MD, USA
| | - Junhui Sun
- Laboratory of Cardiac Physiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xufeng Wu
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, MD, USA
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Corey Smith
- Department of Radiology, University of Chicago, Chicago, IL, USA
| | - Lingyu Bao
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yilun Sun
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Leighton H Duncan
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Elizabeth Murphy
- Laboratory of Cardiac Physiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sougata Roy
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Arpita Upadhyaya
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
| | - Daniel Colón-Ramos
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
- Instituto de Neurobiología, Recinto de Ciencias Médicas, Universidad de Puerto Rico, San Juan, Puerto Rico
| | - Patrick La Riviere
- Department of Radiology, University of Chicago, Chicago, IL, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
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109
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Wang Y, Pinkard H, Khwaja E, Zhou S, Waller L, Huang B. Image denoising for fluorescence microscopy by supervised to self-supervised transfer learning. OPTICS EXPRESS 2021; 29:41303. [PMCID: PMC8970695 DOI: 10.1364/oe.434191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/14/2021] [Accepted: 11/02/2021] [Indexed: 06/18/2023]
Abstract
When using fluorescent microscopy to study cellular dynamics, trade-offs typically have to be made between light exposure and quality of recorded image to balance the phototoxicity and image signal-to-noise ratio. Image denoising is an important tool for retrieving information from dim cell images. Recently, deep learning based image denoising is becoming the leading method because of its promising denoising performance, achieved by leveraging available prior knowledge about the noise model and samples at hand. We demonstrate that incorporating temporal information in the model can further improve the results. However, the practical application of this method has seen challenges because of the requirement of large, task-specific training datasets. In this work, we addressed this challenge by combining self-supervised learning with transfer learning, which eliminated the demand of task-matched training data while maintaining denoising performance. We demonstrate its application in fluorescent imaging of different subcellular structures.
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Affiliation(s)
- Yina Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Henry Pinkard
- Computational Biology Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
- Berkeley Institute for Data Science, Berkeley, CA 94720, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emaad Khwaja
- UC Berkeley - UCSF Joint Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Shuqin Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
- School of Pharmacy, Tsinghua University, Beijing, China
| | - Laura Waller
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
- Berkeley Institute for Data Science, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
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110
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Narcisse D, Mustafi SM, Carlson M, Batabyal S, Kim S, Wright W, Kumar Mohanty S. Bioluminescent Multi-Characteristic Opsin for Simultaneous Optical Stimulation and Continuous Monitoring of Cortical Activities. Front Cell Neurosci 2021; 15:750663. [PMID: 34759801 PMCID: PMC8573050 DOI: 10.3389/fncel.2021.750663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/20/2021] [Indexed: 12/02/2022] Open
Abstract
Stimulation and continuous monitoring of neural activities at cellular resolution are required for the understanding of the sensory processing of stimuli and development of effective neuromodulation therapies. We present bioluminescence multi-characteristic opsin (bMCOII), a hybrid optogenetic actuator, and a bioluminescence Ca2+ sensor for excitation-free, continuous monitoring of neural activities in the visual cortex, with high spatiotemporal resolution. An exceptionally low intensity (10 μW/mm2) of light could elicit neural activation that could be detected by Ca2+ bioluminescence imaging. An uninterrupted (>14 h) recording of visually evoked neural activities in the cortex of mice enabled the determination of strength of sensory activation. Furthermore, an artificial intelligence-based neural activation parameter transformed Ca2+ bioluminescence signals to network activity patterns. During continuous Ca2+-bioluminescence recordings, visual cortical activity peaked at the seventh to eighth hour of anesthesia, coinciding with circadian rhythm. For both direct optogenetic stimulation in cortical slices and visually evoked activities in the visual cortex, we observed secondary delayed Ca2+-bioluminescence responses, suggesting the involvement of neuron-astrocyte-neuron pathway. Our approach will enable the development of a modular and scalable interface system capable of serving a multiplicity of applications to modulate and monitor large-scale activities in the brain.
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Affiliation(s)
| | | | | | | | - Sanghoon Kim
- Nanoscope Technologies LLC, Bedford, TX, United States
| | - Weldon Wright
- Nanoscope Technologies LLC, Bedford, TX, United States
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111
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Xiong B, Zhu T, Xiang Y, Li X, Yu J, Jiang Z, Niu Y, Jiang D, Zhang X, Fang L, Wu J, Dai Q. Mirror-enhanced scanning light-field microscopy for long-term high-speed 3D imaging with isotropic resolution. LIGHT, SCIENCE & APPLICATIONS 2021; 10:227. [PMID: 34737265 PMCID: PMC8568963 DOI: 10.1038/s41377-021-00665-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 05/05/2023]
Abstract
Various biological behaviors can only be observed in 3D at high speed over the long term with low phototoxicity. Light-field microscopy (LFM) provides an elegant compact solution to record 3D information in a tomographic manner simultaneously, which can facilitate high photon efficiency. However, LFM still suffers from the missing-cone problem, leading to degraded axial resolution and ringing effects after deconvolution. Here, we propose a mirror-enhanced scanning LFM (MiSLFM) to achieve long-term high-speed 3D imaging at super-resolved axial resolution with a single objective, by fully exploiting the extended depth of field of LFM with a tilted mirror placed below samples. To establish the unique capabilities of MiSLFM, we performed extensive experiments, we observed various organelle interactions and intercellular interactions in different types of photosensitive cells under extremely low light conditions. Moreover, we demonstrated that superior axial resolution facilitates more robust blood cell tracking in zebrafish larvae at high speed.
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Affiliation(s)
- Bo Xiong
- Department of Automation, Tsinghua University, Beijing, 100084, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, 100084, China
| | - Tianyi Zhu
- Department of Automation, Tsinghua University, Beijing, 100084, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, 100084, China
| | - Yuhan Xiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaopeng Li
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinqiang Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zheng Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yihan Niu
- Department of Automation, Tsinghua University, Beijing, 100084, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, 100084, China
| | - Dong Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Zhang
- Beijing Institute of Collaborative Innovation, Beijing, 100094, China
| | - Lu Fang
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China.
- Department of Electronic Engineering, Tsinghua University, Beijing, 100084, China.
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, 100084, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, 100084, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, 100084, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, 100084, China.
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112
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Zhang W, Du B, Gao M, Tung CH. A Hybrid Nanogel to Preserve Lysosome Integrity for Fluorescence Imaging. ACS NANO 2021; 15:16442-16451. [PMID: 34612039 DOI: 10.1021/acsnano.1c05864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fluorescence imaging of lysosomes provides a powerful tool to probe the lysosome physiology in living cells, yet the continuous light exposure inevitably causes lysosome damage and phototoxicity, which remains a formidable challenge. Here the long-term lysosome tracking with minimized photodamage was realized using a multifunctional nanoprobe, a platinum nanoparticle, and a quinacrine co-loaded nanogel. To construct the hybrid nanogel, cisplatin first functioned as cross-linker to withhold all components and then was reduced to a platinum nanoparticle in situ by ethanol. The platinum nanoparticle enabled a long-term quinacrine fluorescence imaging of lysosome by scavenging the light induced reactive oxygen species which could damage lysosomal membranes.
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Affiliation(s)
- Weiqi Zhang
- State Key Laboratory of Medical Molecular Biology & Department of Biomedical Engineering, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, People's Republic of China
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Baoji Du
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Menghan Gao
- State Key Laboratory of Medical Molecular Biology & Department of Biomedical Engineering, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, People's Republic of China
| | - Ching-Hsuan Tung
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine, New York, New York 10065, United States
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113
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Xu P, Hu L, Yu C, Yang W, Kang F, Zhang M, Jiang P, Wang J. Unsymmetrical cyanine dye via in vivo hitchhiking endogenous albumin affords high-performance NIR-II/photoacoustic imaging and photothermal therapy. J Nanobiotechnology 2021; 19:334. [PMID: 34689764 PMCID: PMC8543934 DOI: 10.1186/s12951-021-01075-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/08/2021] [Indexed: 12/23/2022] Open
Abstract
Herein, an unprecedented synergistic strategy for the development of high-performance NIR-II fluorophore is proposed and validated. Based on an unsymmetrical cyanine dye design strategy, the NIR-II emissive dye NIC was successfully developed by replacing only one of the indoline donors of symmetrical cyanine dye ICG with a fully conjugated benz[c,d]indole donor. This minor structural change maximally maintains the high extinction coefficient advantage of cyanine dyes. NIC-ER with endogenous albumin-hitchhiking capability was constructed to further enhance its in vivo fluorescence brightness. In the presence of HSA (Human serum albumin), NIC-ER spontaneously resides in the albumin pocket, and a brilliant ~89-fold increase in fluorescence was observed. Due to its high molar absorptivity and moderate quantum yield, NIC-ER in HSA exhibits bright NIR-II emission with high photostability and significant Stokes shift (>110 nm). Moreover, NIC-ER was successfully employed for tumor-targeted NIR-II/PA imaging and efficient photothermal tumor elimination. Overall, our strategy may open up a new avenue for designing and constructing high-performance NIR-II fluorophores. ![]()
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Affiliation(s)
- Pengfei Xu
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, #127 West Changle Road, Shanxi, 710032, Xi'an, People's Republic of China.,Institute of Clinical Pharmacy and Pharmacology, Jining First People's Hospital, Jining Medical University, Jining, 272000, People's Republic of China
| | - Linan Hu
- Departments of Radiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, People's Republic of China
| | - Cheng Yu
- Departments of Radiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, People's Republic of China
| | - Weidong Yang
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, #127 West Changle Road, Shanxi, 710032, Xi'an, People's Republic of China
| | - Fei Kang
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, #127 West Changle Road, Shanxi, 710032, Xi'an, People's Republic of China
| | - Mingru Zhang
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, #127 West Changle Road, Shanxi, 710032, Xi'an, People's Republic of China
| | - Pei Jiang
- Institute of Clinical Pharmacy and Pharmacology, Jining First People's Hospital, Jining Medical University, Jining, 272000, People's Republic of China.
| | - Jing Wang
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, #127 West Changle Road, Shanxi, 710032, Xi'an, People's Republic of China.
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A Multi-Modal Toolkit for Studying Neutrophils in Cancer and Beyond. Cancers (Basel) 2021; 13:cancers13215331. [PMID: 34771495 PMCID: PMC8582456 DOI: 10.3390/cancers13215331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Neutrophils are critical immune cells in host defense and maintenance of tissue homeostasis. Studying the complex and diverse functions of these innate immune cells requires a comprehensive toolkit of experimental techniques to elucidate the function and regulation of neutrophils in health and disease. In this review, we discuss key methodologies and their applications in neutrophil research, including in vivo imaging, ex vivo functional assays, and high dimensional single-cell technologies, and how they can be integrated into a multi-modal approach to study neutrophil function in cancer and other diseases. Abstract As key effector cells of the innate immune response, neutrophils are rapidly deployed to sites of inflammation where they deliver a payload of potent effector mechanisms that are essential for host defense against pathogens as well as tissue homeostasis. In addition, neutrophils are central contributors to the pathogenesis of a vast spectrum of inflammatory, degenerative, and neoplastic diseases. As our understanding of neutrophils in health and disease continually expands, so too does our appreciation of their complex and dynamic nature in vivo; from development, maturation, and trafficking to cellular heterogeneity and functional plasticity. Therefore, contemporary neutrophil research relies on multiple complementary methodologies to perform integrated analysis of neutrophil phenotypic heterogeneity, organ- and stimulus-specific trafficking mechanisms, as well as tailored effector functions in vivo. This review discusses established and emerging technologies used to study neutrophils, with a focus on in vivo imaging in animal models, as well as next-generation ex vivo model systems to study mechanisms of neutrophil function. Furthermore, we discuss how high-dimensional single-cell analysis technologies are driving a renaissance in neutrophil biology by redefining our understanding of neutrophil development, heterogeneity, and functional plasticity. Finally, we discuss innovative applications and emerging opportunities to integrate these high-dimensional, multi-modal techniques to deepen our understanding of neutrophils in cancer research and beyond.
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Abstract
Nonlinear optical (NLO) microscopy relies on multiple light-matter interactions to provide unique contrast mechanisms and imaging capabilities that are inaccessible to traditional linear optical imaging approaches, making them versatile tools to understand a wide range of complex systems. However, the strong excitation fields that are necessary to drive higher-order optical processes efficiently are often responsible for photobleaching, photodegradation, and interruption in many systems of interest. This is especially true for imaging living biological samples over prolonged periods of time or in accessing intrinsic dynamics of electronic excited-state processes in spatially heterogeneous materials. This perspective outlines some of the key limitations of two NLO imaging modalities implemented in our lab and highlights the unique potential afforded by the quantum properties of light, especially entangled two-photon absorption based NLO spectroscopy and microscopy. We further review some of the recent exciting advances in this emerging filed and highlight some major challenges facing the realization of quantum-light-enabled NLO imaging modalities.
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Affiliation(s)
- Ying-Zhong Ma
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Benjamin Doughty
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Grenzi M, Resentini F, Vanneste S, Zottini M, Bassi A, Costa A. Illuminating the hidden world of calcium ions in plants with a universe of indicators. PLANT PHYSIOLOGY 2021; 187:550-571. [PMID: 35237821 PMCID: PMC8491032 DOI: 10.1093/plphys/kiab339] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/15/2021] [Indexed: 05/20/2023]
Abstract
The tools available to carry out in vivo analysis of Ca2+ dynamics in plants are powerful and mature technologies that still require the proper controls.
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Affiliation(s)
- Matteo Grenzi
- Department of Biosciences, University of Milan, 20133 Milano, Italy
| | | | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 21985, South Korea
| | - Michela Zottini
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Andrea Bassi
- Department of Physics, Politecnico di Milano, 20133 Milano, Italy
- Institute of Photonics and Nanotechnologies, National Research Council of Italy (CNR), 20133 Milano, Italy
| | - Alex Costa
- Department of Biosciences, University of Milan, 20133 Milano, Italy
- Institute of Biophysics, National Research Council of Italy (CNR), 20133 Milano, Italy
- Author for communication:
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Boka AP, Mukherjee A, Mir M. Single-molecule tracking technologies for quantifying the dynamics of gene regulation in cells, tissue and embryos. Development 2021; 148:272071. [PMID: 34490887 DOI: 10.1242/dev.199744] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
For decades, we have relied on population and time-averaged snapshots of dynamic molecular scale events to understand how genes are regulated during development and beyond. The advent of techniques to observe single-molecule kinetics in increasingly endogenous contexts, progressing from in vitro studies to living embryos, has revealed how much we have missed. Here, we provide an accessible overview of the rapidly expanding family of technologies for single-molecule tracking (SMT), with the goal of enabling the reader to critically analyse single-molecule studies, as well as to inspire the application of SMT to their own work. We start by overviewing the basics of and motivation for SMT experiments, and the trade-offs involved when optimizing parameters. We then cover key technologies, including fluorescent labelling, excitation and detection optics, localization and tracking algorithms, and data analysis. Finally, we provide a summary of selected recent applications of SMT to study the dynamics of gene regulation.
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Affiliation(s)
- Alan P Boka
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Apratim Mukherjee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mustafa Mir
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Hobson CM, Aaron JS, Heddleston JM, Chew TL. Visualizing the Invisible: Advanced Optical Microscopy as a Tool to Measure Biomechanical Forces. Front Cell Dev Biol 2021; 9:706126. [PMID: 34552926 PMCID: PMC8450411 DOI: 10.3389/fcell.2021.706126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/09/2021] [Indexed: 01/28/2023] Open
Abstract
The importance of mechanical force in biology is evident across diverse length scales, ranging from tissue morphogenesis during embryo development to mechanotransduction across single adhesion proteins at the cell surface. Consequently, many force measurement techniques rely on optical microscopy to measure forces being applied by cells on their environment, to visualize specimen deformations due to external forces, or even to directly apply a physical perturbation to the sample via photoablation or optogenetic tools. Recent developments in advanced microscopy offer improved approaches to enhance spatiotemporal resolution, imaging depth, and sample viability. These advances can be coupled with already existing force measurement methods to improve sensitivity, duration and speed, amongst other parameters. However, gaining access to advanced microscopy instrumentation and the expertise necessary to extract meaningful insights from these techniques is an unavoidable hurdle. In this Live Cell Imaging special issue Review, we survey common microscopy-based force measurement techniques and examine how they can be bolstered by emerging microscopy methods. We further explore challenges related to the accompanying data analysis in biomechanical studies and discuss the various resources available to tackle the global issue of technology dissemination, an important avenue for biologists to gain access to pre-commercial instruments that can be leveraged for biomechanical studies.
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Affiliation(s)
- Chad M. Hobson
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
| | - Jesse S. Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
| | - John M. Heddleston
- Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, FL, United States
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
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Verduijn J, Van der Meeren L, Krysko DV, Skirtach AG. Deep learning with digital holographic microscopy discriminates apoptosis and necroptosis. Cell Death Dis 2021; 7:229. [PMID: 34475384 PMCID: PMC8413278 DOI: 10.1038/s41420-021-00616-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023]
Abstract
Regulated cell death modalities such as apoptosis and necroptosis play an important role in regulating different cellular processes. Currently, regulated cell death is identified using the golden standard techniques such as fluorescence microscopy and flow cytometry. However, they require fluorescent labels, which are potentially phototoxic. Therefore, there is a need for the development of new label-free methods. In this work, we apply Digital Holographic Microscopy (DHM) coupled with a deep learning algorithm to distinguish between alive, apoptotic and necroptotic cells in murine cancer cells. This method is solely based on label-free quantitative phase images, where the phase delay of light by cells is quantified and is used to calculate their topography. We show that a combination of label-free DHM in a high-throughput set-up (~10,000 cells per condition) can discriminate between apoptosis, necroptosis and alive cells in the L929sAhFas cell line with a precision of over 85%. To the best of our knowledge, this is the first time deep learning in the form of convolutional neural networks is applied to distinguish-with a high accuracy-apoptosis and necroptosis and alive cancer cells from each other in a label-free manner. It is expected that the approach described here will have a profound impact on research in regulated cell death, biomedicine and the field of (cancer) cell biology in general.
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Affiliation(s)
- Joost Verduijn
- grid.5342.00000 0001 2069 7798Nano-Biotechnology Laboratory, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium ,grid.510942.bCancer Research Institute Ghent, 9000 Ghent, Belgium
| | - Louis Van der Meeren
- grid.5342.00000 0001 2069 7798Nano-Biotechnology Laboratory, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium ,grid.510942.bCancer Research Institute Ghent, 9000 Ghent, Belgium
| | - Dmitri V. Krysko
- grid.510942.bCancer Research Institute Ghent, 9000 Ghent, Belgium ,grid.5342.00000 0001 2069 7798Cell Death Investigation and Therapy (CDIT) Laboratory, Anatomy an Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium ,grid.448878.f0000 0001 2288 8774Department of Pathophysiology, Sechenov First Moscow State Medical University (Sechenov University), 119146 Moscow, Russian Federation
| | - André G. Skirtach
- grid.5342.00000 0001 2069 7798Nano-Biotechnology Laboratory, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium ,grid.510942.bCancer Research Institute Ghent, 9000 Ghent, Belgium
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Liang N, Huang Z, Yan C, Wang K, Kuang D. Lattice light sheets generated with a firmly arranged dielectric regular hexagonal pyramid array. OPTICS LETTERS 2021; 46:4100-4103. [PMID: 34469949 DOI: 10.1364/ol.434299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
We present a firmly arranged dielectric regular hexagonal pyramid array to generate lattice light sheets with high conversion efficiency and low stray light. Both the size and working distance of the lattice light sheets can be modulated by changing the structural parameters. We experimentally recorded the lattice light sheets illumination, which is consistent with the corresponding simulation. To evaluate the imaging quality, we compared the light field generated with and without structure by using polystyrene fluorescent microspheres. This study provides a potential method for the building of light sheet fluorescence microscopy with high resolution and low phototoxicity.
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121
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Yang T, Luo Y, Ji W, Yang G. Advancing biological super-resolution microscopy through deep learning: a brief review. BIOPHYSICS REPORTS 2021; 7:253-266. [PMID: 37287757 PMCID: PMC10233474 DOI: 10.52601/bpr.2021.210019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/22/2021] [Indexed: 06/09/2023] Open
Abstract
Biological super-resolution microscopy is a new generation of imaging techniques that overcome the ~200 nm diffraction limit of conventional light microscopy in spatial resolution. By providing novel spatial or spatiotemporal information on biological processes at nanometer resolution with molecular specificity, it plays an increasingly important role in biomedical sciences. However, its technical constraints also require trade-offs to balance its spatial resolution, temporal resolution, and light exposure of samples. Recently, deep learning has achieved breakthrough performance in many image processing and computer vision tasks. It has also shown great promise in pushing the performance envelope of biological super-resolution microscopy. In this brief review, we survey recent advances in using deep learning to enhance the performance of biological super-resolution microscopy, focusing primarily on computational reconstruction of super-resolution images. Related key technical challenges are discussed. Despite the challenges, deep learning is expected to play an important role in the development of biological super-resolution microscopy. We conclude with an outlook into the future of this new research area.
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Affiliation(s)
- Tianjie Yang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory of Computational Biology and Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yaoru Luo
- Laboratory of Computational Biology and Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100190, China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Wei Ji
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ge Yang
- Laboratory of Computational Biology and Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100190, China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
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122
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Spectroscopic Approach to Correction and Visualisation of Bright-Field Light Transmission Microscopy Biological Data. PHOTONICS 2021. [DOI: 10.3390/photonics8080333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The most realistic information about a transparent sample such as a live cell can be obtained using bright-field light microscopy. Under high-intensity pulsing LED illumination, we captured a primary 12-bit-per-channel (bpc) response from an observed sample using a bright-field microscope equipped with a high-resolution (4872 × 3248) image sensor. In order to suppress data distortions originating from the light interactions with elements in the optical path, poor sensor reproduction (geometrical defects of the camera sensor and some peculiarities of sensor sensitivity), we propose a spectroscopic approach for the correction of these uncompressed 12 bpc data by simultaneous calibration of all parts of the experimental arrangement. Moreover, the final intensities of the corrected images are proportional to the photon fluxes detected by a camera sensor. It can be visualized in 8 bpc intensity depth after the Least Information Loss compression.
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123
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Vargas-Ordaz EJ, Gorelick S, York HM, Liu B, Halls ML, Arumugam S, Neild A, de Marco A, Cadarso VJ. Three-dimensional imaging on a chip using optofluidics light-sheet fluorescence microscopy. LAB ON A CHIP 2021; 21:2945-2954. [PMID: 34124739 DOI: 10.1039/d1lc00098e] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Volumetric, sub-micron to micron level resolution imaging is necessary to assay phenotypes or characteristics at the sub-cellular/organelle scale. However, three-dimensional fluorescence imaging of cells is typically low throughput or compromises on the achievable resolution in space and time. Here, we capitalise on the flow control capabilities of microfluidics and combine it with microoptics to integrate light-sheet based imaging directly into a microfluidic chip. Our optofluidic system flows suspended cells through a sub-micrometer thick light-sheet formed using micro-optical components that are cast directly in polydimethylsiloxane (PDMS). This design ensures accurate alignment, drift-free operation, and easy integration with conventional microfluidics, while providing sufficient spatial resolution, optical sectioning and volumetric data acquisition. We demonstrate imaging rates of 120 ms per cell at sub-μm resolution, that allow extraction of complex cellular phenotypes, exemplified by imaging of cell clusters, receptor distribution, and the analysis of endosomal size changes.
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Affiliation(s)
- Erick J Vargas-Ordaz
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia. and Centre to Impact Antimicrobial Resistance - Sustainable Solutions, Monash University, Clayton, 3800, Victoria, Australia
| | - Sergey Gorelick
- Department of Biochemistry and Molecular Biology, Monash University, 3800 Clayton, Victoria, Australia. and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia
| | - Harrison M York
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia and European Molecular Biology Laboratory (EMBL) Australia, Monash University, 3800 Clayton, Victoria, Australia and Department of Anatomy and Developmental Biology, Monash University, 3800 Clayton, Victoria, Australia
| | - Bonan Liu
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Michelle L Halls
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Senthil Arumugam
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia and European Molecular Biology Laboratory (EMBL) Australia, Monash University, 3800 Clayton, Victoria, Australia and Department of Anatomy and Developmental Biology, Monash University, 3800 Clayton, Victoria, Australia
| | - Adrian Neild
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Monash University, 3800 Clayton, Victoria, Australia. and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia
| | - Victor J Cadarso
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia. and Centre to Impact Antimicrobial Resistance - Sustainable Solutions, Monash University, Clayton, 3800, Victoria, Australia and The Melbourne Centre for Nanofabrication, Victorian Node - Australian National Fabrication Facility, Clayton, Victoria 3800, Australia
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Larsen JB, Taebnia N, Dolatshahi-Pirouz A, Eriksen AZ, Hjørringgaard C, Kristensen K, Larsen NW, Larsen NB, Marie R, Mündler AK, Parhamifar L, Urquhart AJ, Weller A, Mortensen KI, Flyvbjerg H, Andresen TL. Imaging therapeutic peptide transport across intestinal barriers. RSC Chem Biol 2021; 2:1115-1143. [PMID: 34458827 PMCID: PMC8341777 DOI: 10.1039/d1cb00024a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Oral delivery is a highly preferred method for drug administration due to high patient compliance. However, oral administration is intrinsically challenging for pharmacologically interesting drug classes, in particular pharmaceutical peptides, due to the biological barriers associated with the gastrointestinal tract. In this review, we start by summarizing the pharmacological performance of several clinically relevant orally administrated therapeutic peptides, highlighting their low bioavailabilities. Thus, there is a strong need to increase the transport of peptide drugs across the intestinal barrier to realize future treatment needs and further development in the field. Currently, progress is hampered by a lack of understanding of transport mechanisms that govern intestinal absorption and transport of peptide drugs, including the effects of the permeability enhancers commonly used to mediate uptake. We describe how, for the past decades, mechanistic insights have predominantly been gained using functional assays with end-point read-out capabilities, which only allow indirect study of peptide transport mechanisms. We then focus on fluorescence imaging that, on the other hand, provides opportunities to directly visualize and thus follow peptide transport at high spatiotemporal resolution. Consequently, it may provide new and detailed mechanistic understanding of the interplay between the physicochemical properties of peptides and cellular processes; an interplay that determines the efficiency of transport. We review current methodology and state of the art in the field of fluorescence imaging to study intestinal barrier transport of peptides, and provide a comprehensive overview of the imaging-compatible in vitro, ex vivo, and in vivo platforms that currently are being developed to accelerate this emerging field of research.
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Affiliation(s)
- Jannik Bruun Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Nayere Taebnia
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Alireza Dolatshahi-Pirouz
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Anne Zebitz Eriksen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Claudia Hjørringgaard
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Kasper Kristensen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Nanna Wichmann Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Niels Bent Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Rodolphe Marie
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Ann-Kathrin Mündler
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Ladan Parhamifar
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Andrew James Urquhart
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Arjen Weller
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Kim I Mortensen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Henrik Flyvbjerg
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Thomas Lars Andresen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
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Li Y, Qin C, Song Y, Yan H, Han S, Zhou H, Wei A, Zhang G, Chen R, Hu J, Jing M, Xiao L, Jia S. Great enhancement on two-photon photoluminescence imaging contrast of Au nanoparticles via double-pulse femtosecond laser excitation with controlled phase differences. OPTICS EXPRESS 2021; 29:22855-22867. [PMID: 34614564 DOI: 10.1364/oe.428428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Au nanoparticles are attractive contrast agents for noninvasive living tissue imaging with deep penetration because of their strong two-photon photoluminescence (TPPL) intensity and excellent biocompatibility. However, the inevitable phototoxicity and huge auto-fluorescence are consistently associated with laser excitation. Therefore, enhancement of TPPL intensity and suppression of backgrounds are always highly desired under the demand of reducing excitation powers. In this work, we develop a double-pulse TPPL (DP-TPPL) scheme with controlled phase differences (Δφ) between the double pulses to significantly improve the signal-to-noise ratio (SNR) of TPPL imaging. Under the modulated phase (Δφ periodically varying between 0-2π), our results show that SNR can be improved from 4.3 to 1715, with an enhancement of up to 400 folds at the integration of 50 ms. More importantly, this enhancement can be unlimitedly lifted by increasing the number of photons or integration times in principle. Further boosting has been achieved by reducing the magnitude of background noises; subsequently, SNR is improved by more than 104 times. Our schemes offer great potential for reducing phototoxicity and extracting extremely weak signals from huge backgrounds and open up a new possibility for a rapid, flexible, and reliable medical diagnosis by TPPL imaging with diminished laser powers.
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Emon MAB, Knoll S, Doha U, Ladehoff L, Lalonde L, Baietto D, Sivaguru M, Bhargava R, Saif MTA. Dose- independent threshold illumination for non-invasive time-lapse fluorescence imaging of live cells. EXTREME MECHANICS LETTERS 2021; 46:101249. [PMID: 34095408 PMCID: PMC8171180 DOI: 10.1016/j.eml.2021.101249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Fluorescent microscopy employs monochromatic light for excitation, which can adversely affect the cells being observed. We reported earlier that fibroblasts relax their contractile force in response to green light of typical intensity. Here we show that such effects are independent of extracellular matrix and cell lines. In addition, we establish a threshold intensity that elicits minimal or no adverse effect on cell contractility even for long-time exposure. This threshold intensity is wavelength dependent. We cultured fibroblasts on soft 2D elastic hydrogels embedded with fluorescent beads to trace substrate deformation and cell forces. The beads move towards cell center when cells contract, but they move away when cells relax. We use relaxation/contraction ratio (λ r), in addition to traction force, as measures of cell response to red (wavelength, λ=635-650 nm), green (λ=545-580 nm) and blue (λ=455-490 nm) lights with varying intensities. Our results suggest that intensities below 57, 31 and 3.5 W/m2 for red, green and blue lights, respectively, do not perturb force homeostasis. To our knowledge, these intensities are the lowest reported safe thresholds, implying that cell traction is a highly sensitive readout of the effect of light on cells. Most importantly, we find these threshold intensities to be dose-independent; i.e., safe regardless of the energy dosage or time of exposure. Conversely, higher intensities result in widespread force-relaxation in cells with λ r > 1. Furthermore, we present a photo-reaction based model that simulates photo-toxicity and predicts threshold intensity for different wavelengths within the visible spectra. In conclusion, we recommend employing illumination intensities below aforementioned wavelength-specific thresholds for time-lapse imaging of cells and tissues in order to avoid light-induced artifacts in experimental observations.
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Affiliation(s)
- M A Bashar Emon
- Dept. of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign
| | - Samantha Knoll
- Dept. of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign
| | - Umnia Doha
- Dept. of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign
| | - Lauren Ladehoff
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign
| | - Luke Lalonde
- Dept. of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign
| | - Danielle Baietto
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign
| | - Mayandi Sivaguru
- Carle Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign
| | - Rohit Bhargava
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign
| | - M Taher A Saif
- Dept. of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign
- Corresponding author: M Taher A Saif, Gutgsell Professor, Associate Head for Graduate Programs and Research, Mechanical Science and Engineering, Research Professor, Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, 2101D Mechanical Engineering Laboratory, 105 S. Mathews Avenue, Urbana, IL 61801, USA, , Tel: 217-333-8552, Fax: 217-244-6534, http://saif.mechse.illinois.edu/
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Valli J, Garcia-Burgos A, Rooney LM, Vale de Melo E Oliveira B, Duncan RR, Rickman C. Seeing beyond the limit: A guide to choosing the right super-resolution microscopy technique. J Biol Chem 2021; 297:100791. [PMID: 34015334 PMCID: PMC8246591 DOI: 10.1016/j.jbc.2021.100791] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023] Open
Abstract
Super-resolution microscopy has become an increasingly popular and robust tool across the life sciences to study minute cellular structures and processes. However, with the increasing number of available super-resolution techniques has come an increased complexity and burden of choice in planning imaging experiments. Choosing the right super-resolution technique to answer a given biological question is vital for understanding and interpreting biological relevance. This is an often-neglected and complex task that should take into account well-defined criteria (e.g., sample type, structure size, imaging requirements). Trade-offs in different imaging capabilities are inevitable; thus, many researchers still find it challenging to select the most suitable technique that will best answer their biological question. This review aims to provide an overview and clarify the concepts underlying the most commonly available super-resolution techniques as well as guide researchers through all aspects that should be considered before opting for a given technique.
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Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom.
| | - Adrian Garcia-Burgos
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Liam M Rooney
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Beatriz Vale de Melo E Oliveira
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Rory R Duncan
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Colin Rickman
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom.
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129
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Chen X, Kandel ME, Popescu G. Spatial light interference microscopy: principle and applications to biomedicine. ADVANCES IN OPTICS AND PHOTONICS 2021; 13:353-425. [PMID: 35494404 PMCID: PMC9048520 DOI: 10.1364/aop.417837] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In this paper, we review spatial light interference microscopy (SLIM), a common-path, phase-shifting interferometer, built onto a phase-contrast microscope, with white-light illumination. As one of the most sensitive quantitative phase imaging (QPI) methods, SLIM allows for speckle-free phase reconstruction with sub-nanometer path-length stability. We first review image formation in QPI, scattering, and full-field methods. Then, we outline SLIM imaging from theory and instrumentation to diffraction tomography. Zernike's phase-contrast microscopy, phase retrieval in SLIM, and halo removal algorithms are discussed. Next, we discuss the requirements for operation, with a focus on software developed in-house for SLIM that enables high-throughput acquisition, whole slide scanning, mosaic tile registration, and imaging with a color camera. We introduce two methods for solving the inverse problem using SLIM, white-light tomography, and Wolf phase tomography. Lastly, we review the applications of SLIM in basic science and clinical studies. SLIM can study cell dynamics, cell growth and proliferation, cell migration, mass transport, etc. In clinical settings, SLIM can assist with cancer studies, reproductive technology, blood testing, etc. Finally, we review an emerging trend, where SLIM imaging in conjunction with artificial intelligence brings computational specificity and, in turn, offers new solutions to outstanding challenges in cell biology and pathology.
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130
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Louey A, Hernández D, Pébay A, Daniszewski M. Automation of Organoid Cultures: Current Protocols and Applications. SLAS DISCOVERY 2021; 26:1138-1147. [PMID: 34167363 DOI: 10.1177/24725552211024547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
GRAPHICAL ABSTRACT [Formula: see text].
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Affiliation(s)
- Alexandra Louey
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
| | - Damián Hernández
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia.,Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
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131
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Wu J, Lu Z, Jiang D, Guo Y, Qiao H, Zhang Y, Zhu T, Cai Y, Zhang X, Zhanghao K, Xie H, Yan T, Zhang G, Li X, Jiang Z, Lin X, Fang L, Zhou B, Xi P, Fan J, Yu L, Dai Q. Iterative tomography with digital adaptive optics permits hour-long intravital observation of 3D subcellular dynamics at millisecond scale. Cell 2021; 184:3318-3332.e17. [PMID: 34038702 DOI: 10.1016/j.cell.2021.04.029] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/04/2021] [Accepted: 04/16/2021] [Indexed: 01/03/2023]
Abstract
Long-term subcellular intravital imaging in mammals is vital to study diverse intercellular behaviors and organelle functions during native physiological processes. However, optical heterogeneity, tissue opacity, and phototoxicity pose great challenges. Here, we propose a computational imaging framework, termed digital adaptive optics scanning light-field mutual iterative tomography (DAOSLIMIT), featuring high-speed, high-resolution 3D imaging, tiled wavefront correction, and low phototoxicity with a compact system. By tomographic imaging of the entire volume simultaneously, we obtained volumetric imaging across 225 × 225 × 16 μm3, with a resolution of up to 220 nm laterally and 400 nm axially, at the millisecond scale, over hundreds of thousands of time points. To establish the capabilities, we investigated large-scale cell migration and neural activities in different species and observed various subcellular dynamics in mammals during neutrophil migration and tumor cell circulation.
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Affiliation(s)
- Jiamin Wu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Zhi Lu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Dong Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuduo Guo
- Department of Electronic Engineering, Tsinghua University, Beijing 100084, China
| | - Hui Qiao
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Yi Zhang
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China
| | - Tianyi Zhu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China
| | - Yeyi Cai
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China
| | - Xu Zhang
- Department of Automation, Tsinghua University, Beijing 100084, China; Beijing Institute of Collaborative Innovation, Beijing 100094, China
| | - Karl Zhanghao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Hao Xie
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Tao Yan
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China
| | - Guoxun Zhang
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China
| | - Xiaoxu Li
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China
| | - Zheng Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xing Lin
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China
| | - Lu Fang
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Department of Electronic Engineering, Tsinghua University, Beijing 100084, China
| | - Bing Zhou
- Advanced Innovation Center for Big Data-based Precision Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Peng Xi
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Jingtao Fan
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
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132
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Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes. Nat Methods 2021; 18:678-687. [PMID: 34059829 DOI: 10.1038/s41592-021-01155-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 04/15/2021] [Indexed: 02/02/2023]
Abstract
We demonstrate residual channel attention networks (RCAN) for the restoration and enhancement of volumetric time-lapse (four-dimensional) fluorescence microscopy data. First we modify RCAN to handle image volumes, showing that our network enables denoising competitive with three other state-of-the-art neural networks. We use RCAN to restore noisy four-dimensional super-resolution data, enabling image capture of over tens of thousands of images (thousands of volumes) without apparent photobleaching. Second, using simulations we show that RCAN enables resolution enhancement equivalent to, or better than, other networks. Third, we exploit RCAN for denoising and resolution improvement in confocal microscopy, enabling ~2.5-fold lateral resolution enhancement using stimulated emission depletion microscopy ground truth. Fourth, we develop methods to improve spatial resolution in structured illumination microscopy using expansion microscopy data as ground truth, achieving improvements of ~1.9-fold laterally and ~3.6-fold axially. Finally, we characterize the limits of denoising and resolution enhancement, suggesting practical benchmarks for evaluation and further enhancement of network performance.
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133
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Hua X, Liu W, Jia S. High-resolution Fourier light-field microscopy for volumetric multi-color live-cell imaging. OPTICA 2021; 8:614-620. [PMID: 34327282 PMCID: PMC8318351 DOI: 10.1364/optica.419236] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Volumetric interrogation of the organization and processes of intracellular organelles and molecules in cellular systems with a high spatiotemporal resolution is essential for understanding cell physiology, development, and pathology. Here, we report high-resolution Fourier light-field microscopy (HR-FLFM) for fast and volumetric live-cell imaging. HR-FLFM transforms conventional cell microscopy and enables exploration of less accessible spatiotemporal-limiting regimes for single-cell studies. The results present a near-diffraction-limited resolution in all three dimensions, a five-fold extended focal depth to several micrometers, and a scanning-free volume acquisition time up to milliseconds. The system demonstrates instrumentation accessibility, low photo damage for continuous observation, and high compatibility with general cell assays. We anticipate HR-FLFM to offer a promising methodological pathway for investigating a wide range of intracellular processes and functions with exquisite spatiotemporal contextual details.
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134
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Harrison SP, Baumgarten SF, Verma R, Lunov O, Dejneka A, Sullivan GJ. Liver Organoids: Recent Developments, Limitations and Potential. Front Med (Lausanne) 2021; 8:574047. [PMID: 34026769 PMCID: PMC8131532 DOI: 10.3389/fmed.2021.574047] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Liver cell types derived from induced pluripotent stem cells (iPSCs) share the potential to investigate development, toxicity, as well as genetic and infectious disease in ways currently limited by the availability of primary tissue. With the added advantage of patient specificity, which can play a role in all of these areas. Many iPSC differentiation protocols focus on 3 dimensional (3D) or organotypic differentiation, as these offer the advantage of more closely mimicking in vivo systems including; the formation of tissue like architecture and interactions/crosstalk between different cell types. Ultimately such models have the potential to be used clinically and either with or more aptly, in place of animal models. Along with the development of organotypic and micro-tissue models, there will be a need to co-develop imaging technologies to enable their visualization. A variety of liver models termed "organoids" have been reported in the literature ranging from simple spheres or cysts of a single cell type, usually hepatocytes, to those containing multiple cell types combined during the differentiation process such as hepatic stellate cells, endothelial cells, and mesenchymal cells, often leading to an improved hepatic phenotype. These allow specific functions or readouts to be examined such as drug metabolism, protein secretion or an improved phenotype, but because of their relative simplicity they lack the flexibility and general applicability of ex vivo tissue culture. In the liver field these are more often constructed rather than developed together organotypically as seen in other organoid models such as brain, kidney, lung and intestine. Having access to organotypic liver like surrogates containing multiple cell types with in vivo like interactions/architecture, would provide vastly improved models for disease, toxicity and drug development, combining disciplines such as microfluidic chip technology with organoids and ultimately paving the way to new therapies.
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Affiliation(s)
- Sean Philip Harrison
- Hybrid Technology Hub–Center of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | - Saphira Felicitas Baumgarten
- Hybrid Technology Hub–Center of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | - Rajneesh Verma
- Hybrid Technology Hub–Center of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | - Oleg Lunov
- Institute of Physics of the Czech Academy of Sciences, Prague, Czechia
| | - Alexandr Dejneka
- Institute of Physics of the Czech Academy of Sciences, Prague, Czechia
| | - Gareth John Sullivan
- Hybrid Technology Hub–Center of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
- Norwegian Center for Stem Cell Research, Oslo University Hospital, University of Oslo, Oslo, Norway
- Institute of Immunology, Oslo University Hospital, Oslo, Norway
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135
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Huang Z, Gu P, Kuang D, Mi P, Feng X. Dynamic imaging of zebrafish heart with multi-planar light sheet microscopy. JOURNAL OF BIOPHOTONICS 2021; 14:e202000466. [PMID: 33452862 DOI: 10.1002/jbio.202000466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/31/2020] [Accepted: 01/13/2021] [Indexed: 05/03/2023]
Abstract
Light sheet fluorescence microscopy has become a research hotspot in biomedicine because of low phototoxicity, high speed, and high resolution. However, the conventional methods to acquire three-dimensional spatial information are mainly based on scanning, which inevitably increases photodamage and is not real-time. Here, we propose a method to generate controllable multi-planar illumination with a dielectric isosceles triangular array and a design of multi-planar light sheet fluorescence microscopy system. We carry out experiments of three-dimensional illumination beam measurement, volumetric imaging of fluorescent microspheres, and dynamic in vivo imaging of zebrafish heart to evaluate the performance of this system. In addition, we apply this system to study the effects of bisphenol fluorene on the heart shape and heart-beating rate of zebrafish. Our experiment results indicate that the multi-planar light sheet microscopy system provides a novel and feasible method for three-dimensional selected plane imaging and low-phototoxicity in vivo imaging.
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Affiliation(s)
- Zengxin Huang
- Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, and Institute of Modern Optics, Nankai University, Tianjin, China
| | - Panchun Gu
- Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, and Institute of Modern Optics, Nankai University, Tianjin, China
| | - Dengfeng Kuang
- Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, and Institute of Modern Optics, Nankai University, Tianjin, China
| | - Ping Mi
- State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Xizeng Feng
- State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
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136
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Feng X, Leong WH, Xia K, Liu CF, Liu GQ, Rendler T, Wrachtrup J, Liu RB, Li Q. Association of Nanodiamond Rotation Dynamics with Cell Activities by Translation-Rotation Tracking. NANO LETTERS 2021; 21:3393-3400. [PMID: 33847115 DOI: 10.1021/acs.nanolett.0c04864] [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] [Indexed: 06/12/2023]
Abstract
Correlated translation-orientation tracking of single particles can provide important information for understanding the dynamics of live systems and their interaction with the probes. However, full six-dimensional (6D) motion tracking has yet to be achieved. Here, we developed synchronized 3D translation and 3D rotation tracking of single diamond particles based on nitrogen-vacancy center sensing. We first performed 6D tracking of diamond particles attached to a giant plasma membrane vesicle to demonstrate the method. Quantitative analysis of diamond particles' motion allowed elimination of the geometric effect and revealed the net rotation on the vesicle. 6D tracking was then applied to measure live cell dynamics. Motion characteristics of nanodiamonds on cell membranes under various controlled physiological conditions suggest that the nanodiamonds' rotation is associated with cell metabolic activities. Our technique extends the toolbox of single particle tracking and provides a unique solution to problems where correlated analysis of translation and rotation is critical.
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Affiliation(s)
- Xi Feng
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Weng-Hang Leong
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Kangwei Xia
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Chu-Feng Liu
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Gang-Qin Liu
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Torsten Rendler
- 3rd Institute of Physics and Center for Applied Quantum Technologies, University of Stuttgart, 70569 Stuttgart, Germany
| | - Joerg Wrachtrup
- 3rd Institute of Physics and Center for Applied Quantum Technologies, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ren-Bao Liu
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- The Hong Kong Institute of Quantum Information Science and Technology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- Centre for Quantum Coherence, The Chinese University of Hong Kong, Hong Kong, China
| | - Quan Li
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- The Hong Kong Institute of Quantum Information Science and Technology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- Centre for Quantum Coherence, The Chinese University of Hong Kong, Hong Kong, China
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Abstract
Surface-enhanced Raman scattering (SERS) nanotags are widely used in the biomedical field including live-cell imaging due to the high specificity from their fingerprint spectrum and the multiplexing capability from the ultra-narrow linewidth. However, long-term live-cell Raman imaging is limited due to the photodamage from a relatively long exposure time and a high laser power, which are needed for acquiring detectable Raman signals. In this work, we attempt to resolve this issue by developing ultrabright gap-enhanced resonance Raman tags (GERRTs), consisting of a petal-like gold core and a silver shell with the near-infrared resonant reporter of IR-780 embedded in between, for long-term and high-speed live-cell imaging. GERRTs exhibit an ultrahigh Raman intensity down to a single-nanoparticle level in aqueous solution and the solid state upon 785 nm excitation, allowing for high-resolution time-lapse live-cell Raman imaging with an exposure time of 1 ms per pixel and a laser power of 50 μW. Under these measurement conditions, we can possibly capture dynamic cellular processes with a high temporal resolution, and track living cells for long periods of time owing to the reduced photodamage to cells. These nanotags open new opportunities for ultrasensitive, low-phototoxic, and long-term live-cell imaging.
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Affiliation(s)
- Yuqing Gu
- Department of Nuclear Medicine, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, P. R. China.
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138
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Optogenetics to Interrogate Neuron-Glia Interactions in Pups and Adults. Methods Mol Biol 2021. [PMID: 32865743 DOI: 10.1007/978-1-0716-0830-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In just over 10 years, the use of optogenetic technologies in neuroscience has become widespread, having today a tremendous impact on our understanding of brain function. An extensive number of studies have implemented a variety of tools allowing for the manipulation of neurons with light, including light-activated ion channels or G protein-coupled receptors, among other innovations. In this context, the proper calibration of photostimulation in vivo remains crucial to dissect brain circuitry or investigate the effect of neuronal activity on specific subpopulations of neurons and glia. Depending on the scientific question, the design of specific stimulation protocols must consider from the choice of the animal model to the light stimulation pattern to be delivered. In this chapter, we describe a detailed framework to investigate neuron-glia interactions in both mouse pups and adults using an optogenetic approach.
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139
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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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140
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Jambor H, Antonietti A, Alicea B, Audisio TL, Auer S, Bhardwaj V, Burgess SJ, Ferling I, Gazda MA, Hoeppner LH, Ilangovan V, Lo H, Olson M, Mohamed SY, Sarabipour S, Varma A, Walavalkar K, Wissink EM, Weissgerber TL. Creating clear and informative image-based figures for scientific publications. PLoS Biol 2021; 19:e3001161. [PMID: 33788834 PMCID: PMC8041175 DOI: 10.1371/journal.pbio.3001161] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/12/2021] [Accepted: 02/26/2021] [Indexed: 11/18/2022] Open
Abstract
Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in 3 fields; plant sciences, cell biology, and physiology (n = 580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.
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Affiliation(s)
- Helena Jambor
- Mildred Scheel Early Career Center, Medical Faculty, Technische Universität Dresden, Dresden, Germany
| | - Alberto Antonietti
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Bradly Alicea
- Orthogonal Research and Education Laboratory, Champaign, IL, United States of America
| | - Tracy L. Audisio
- Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Susann Auer
- Department of Plant Physiology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Vivek Bhardwaj
- Max Plank Institute of Immunology and Epigenetics, Freiburg, Germany
- Hubrecht Institute, Utrecht, the Netherlands
| | - Steven J. Burgess
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Iuliia Ferling
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute (HKI), Jena, Germany
| | - Małgorzata Anna Gazda
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Luke H. Hoeppner
- The Hormel Institute, University of Minnesota, Austin, MN, United States of America
- The Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | | | - Hung Lo
- Neuroscience Research Center, Charité—Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt—Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
- Einstein Center for Neurosciences Berlin, Berlin, Germany
| | - Mischa Olson
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
| | - Salem Yousef Mohamed
- Gastroenterology and Hepatology Unit, Internal Medicine Department, Faculty of Medicine, University of Zagazig, Zagazig, Egypt
| | - Sarvenaz Sarabipour
- Institute for Computational Medicine and the Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Aalok Varma
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore, Karnataka, India
| | - Kaivalya Walavalkar
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore, Karnataka, India
| | - Erin M. Wissink
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Tracey L. Weissgerber
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, QUEST Center, Berlin, Germany
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141
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Kiraga Ł, Kucharzewska P, Strzemecki D, Rygiel TP, Król M. Non-radioactive imaging strategies for in vivo immune cell tracking. PHYSICAL SCIENCES REVIEWS 2021; 8:385-403. [PMID: 36975764 PMCID: PMC10037928 DOI: 10.1515/psr-2020-0205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In vivo tracking of administered cells chosen for specific disease treatment may be conducted by diagnostic imaging techniques preceded by cell labeling with special contrast agents. The most commonly used agents are those with radioactive properties, however their use in research is often impossible. This review paper focuses on the essential aspect of cell tracking with the exclusion of radioisotope tracers, therefore we compare application of different types of non-radioactive contrast agents (cell tracers), methods of cell labeling and application of various techniques for cell tracking, which are commonly used in preclinical or clinical studies. We discuss diagnostic imaging methods belonging to three groups: (1) Contrast-enhanced X-ray imaging, (2) Magnetic resonance imaging, and (3) Optical imaging. In addition, we present some interesting data from our own research on tracking immune cell with the use of discussed methods. Finally, we introduce an algorithm which may be useful for researchers planning leukocyte targeting studies, which may help to choose the appropriate cell type, contrast agent and diagnostic technique for particular disease study.
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Affiliation(s)
- Łukasz Kiraga
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
- Cellis AG, 80002 Zurich, Switzerland
| | - Paulina Kucharzewska
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
- Cellis AG, 80002 Zurich, Switzerland
| | | | - Tomasz P. Rygiel
- Cellis AG, 80002 Zurich, Switzerland
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Magdalena Król
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
- Cellis AG, 80002 Zurich, Switzerland
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142
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143
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Klymchenko AS, Liu F, Collot M, Anton N. Dye-Loaded Nanoemulsions: Biomimetic Fluorescent Nanocarriers for Bioimaging and Nanomedicine. Adv Healthc Mater 2021; 10:e2001289. [PMID: 33052037 DOI: 10.1002/adhm.202001289] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Indexed: 12/16/2022]
Abstract
Lipid nanoemulsions (NEs), owing to their controllable size (20 to 500 nm), stability and biocompatibility, are now frequently used in various fields, such as food, cosmetics, pharmaceuticals, drug delivery, and even as nanoreactors for chemical synthesis. Moreover, being composed of components generally recognized as safe (GRAS), they can be considered as "green" nanoparticles that mimic closely lipoproteins and intracellular lipid droplets. Therefore, they attracted attention as carriers of drugs and fluorescent dyes for both bioimaging and studying the fate of nanoemulsions in cells and small animals. In this review, the composition of dye-loaded NEs, methods for their preparation, and emerging biological applications are described. The design of bright fluorescent NEs with high dye loading and minimal aggregation-caused quenching (ACQ) is focused on. Common issues including dye leakage and NEs stability are discussed, highlighting advanced techniques for their characterization, such as Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS). Attempts to functionalize NEs surface are also discussed. Thereafter, biological applications for bioimaging and single-particle tracking in cells and small animals as well as biomedical applications for photodynamic therapy are described. Finally, challenges and future perspectives of fluorescent NEs are discussed.
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Affiliation(s)
- Andrey S. Klymchenko
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
| | - Fei Liu
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
- Université de Strasbourg CNRS CAMB UMR 7199 Strasbourg F‐67000 France
| | - Mayeul Collot
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
| | - Nicolas Anton
- Université de Strasbourg CNRS CAMB UMR 7199 Strasbourg F‐67000 France
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144
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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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145
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Taylor RW, Holler C, Mahmoodabadi RG, Küppers M, Dastjerdi HM, Zaburdaev V, Schambony A, Sandoghdar V. High-Precision Protein-Tracking With Interferometric Scattering Microscopy. Front Cell Dev Biol 2020; 8:590158. [PMID: 33224953 PMCID: PMC7669747 DOI: 10.3389/fcell.2020.590158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/05/2020] [Indexed: 01/01/2023] Open
Abstract
The mobility of proteins and lipids within the cell, sculpted oftentimes by the organization of the membrane, reveals a great wealth of information on the function and interaction of these molecules as well as the membrane itself. Single particle tracking has proven to be a vital tool to study the mobility of individual molecules and unravel details of their behavior. Interferometric scattering (iSCAT) microscopy is an emerging technique well-suited for visualizing the diffusion of gold nanoparticle-labeled membrane proteins to a spatial and temporal resolution beyond the means of traditional fluorescent labels. We discuss the applicability of interferometric single particle tracking (iSPT) microscopy to investigate the minutia in the motion of a protein through measurements visualizing the mobility of the epidermal growth factor receptor in various biological scenarios on the live cell.
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Affiliation(s)
- Richard W Taylor
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Cornelia Holler
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Reza Gholami Mahmoodabadi
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Michelle Küppers
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Department of Physics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Houman Mirzaalian Dastjerdi
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Department of Computer Science, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Vasily Zaburdaev
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Department of Biology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Alexandra Schambony
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Department of Biology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Department of Physics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
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146
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Bai S, Yang N, Wang X, Gong F, Dong Z, Gong Y, Liu Z, Cheng L. Ultrasmall Iron-Doped Titanium Oxide Nanodots for Enhanced Sonodynamic and Chemodynamic Cancer Therapy. ACS NANO 2020; 14:15119-15130. [PMID: 33185089 DOI: 10.1021/acsnano.0c05235] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sonodynamic therapy (SDT), which can generate reactive oxygen species (ROS) based on sonosensitizers under ultrasound (US) to kill tumor cells, has emerged as a noninvasive therapeutic modality with high tissue-penetration depth. Herein, ultrasmall iron-doped titanium oxide nanodots (Fe-TiO2 NDs) are synthesized via a thermal decomposition strategy as a type of sonosensitizers to enhance SDT. Interestingly, the Fe doping in this system appears to be crucial in not only enhancing the US-triggered ROS generation of those NDs but also offering NDs the Fenton-catalytic function to generate ROS from tumor endogenous H2O2 for chemodynamic therapy (CDT). After polyethylene glycol (PEG) modification, Fe-TiO2-PEG NDs demonstrate good physiological stability and biocompatibility. With efficient tumor retention after intravenous injection as revealed by in vivo magnetic resonance (MR) and fluorescent imaging, our Fe-TiO2 NDs demonstrate much better in vivo therapeutic performance than commercial TiO2 nanoparticles owing to the combination of CDT and SDT. Moreover, most of those ultrasmall Fe-TiO2 NDs can be effectively excreted within one month, rendering no obvious long-term toxicity to the treated mice. Our work thus presents a type of multifunctional sonosensitizer for highly efficient cancer treatment via simply doping TiO2 nanostructures with metal ions.
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Affiliation(s)
- Shang Bai
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, People's Republic of China
| | - Nailin Yang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, People's Republic of China
| | - Xianwen Wang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, People's Republic of China
| | - Fei Gong
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, People's Republic of China
| | - Ziliang Dong
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, People's Republic of China
| | - Yuehan Gong
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, People's Republic of China
| | - Zhuang Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, People's Republic of China
| | - Liang Cheng
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, People's Republic of China
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147
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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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148
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Maioli V, Boniface A, Mahou P, Ortas JF, Abdeladim L, Beaurepaire E, Supatto W. Fast in vivo multiphoton light-sheet microscopy with optimal pulse frequency. BIOMEDICAL OPTICS EXPRESS 2020; 11:6012-6026. [PMID: 33150002 PMCID: PMC7587280 DOI: 10.1364/boe.400113] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 05/05/2023]
Abstract
Improving the imaging speed of multiphoton microscopy is an active research field. Among recent strategies, light-sheet illumination holds distinctive advantages for achieving fast imaging in vivo. However, photoperturbation in multiphoton light-sheet microscopy remains poorly investigated. We show here that the heart beat rate of zebrafish embryos is a sensitive probe of linear and nonlinear photoperturbations. By analyzing its behavior with respect to laser power, pulse frequency and wavelength, we derive guidelines to find the best balance between signal and photoperturbation. We then demonstrate one order-of-magnitude signal enhancement over previous implementations by optimizing the laser pulse frequency. These results open new opportunities for fast live tissue imaging.
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Affiliation(s)
- Vincent Maioli
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Antoine Boniface
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Júlia Ferrer Ortas
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Lamiae Abdeladim
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Willy Supatto
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
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149
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Versatile live-cell activity analysis platform for characterization of neuronal dynamics at single-cell and network level. Nat Commun 2020; 11:4854. [PMID: 32978383 PMCID: PMC7519655 DOI: 10.1038/s41467-020-18620-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Chronic imaging of neuronal networks in vitro has provided fundamental insights into mechanisms underlying neuronal function. Current labeling and optical imaging methods, however, cannot be used for continuous and long-term recordings of the dynamics and evolution of neuronal networks, as fluorescent indicators can cause phototoxicity. Here, we introduce a versatile platform for label-free, comprehensive and detailed electrophysiological live-cell imaging of various neurogenic cells and tissues over extended time scales. We report on a dual-mode high-density microelectrode array, which can simultaneously record in (i) full-frame mode with 19,584 recording sites and (ii) high-signal-to-noise mode with 246 channels. We set out to demonstrate the capabilities of this platform with recordings from primary and iPSC-derived neuronal cultures and tissue preparations over several weeks, providing detailed morpho-electrical phenotypic parameters at subcellular, cellular and network level. Moreover, we develop reliable analysis tools, which drastically increase the throughput to infer axonal morphology and conduction speed. Current methods of neuronal network imaging cannot be used for continuous, long-term functional recordings. Here, the authors present a dual-mode high-density microelectrode array, which can simultaneously record in full-frame and high-signal-to-noise modes for label-free electrophysiological measurements.
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150
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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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