101
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Cuny AP, Schlottmann FP, Ewald JC, Pelet S, Schmoller KM. Live cell microscopy: From image to insight. BIOPHYSICS REVIEWS 2022; 3:021302. [PMID: 38505412 PMCID: PMC10903399 DOI: 10.1063/5.0082799] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/18/2022] [Indexed: 03/21/2024]
Abstract
Live-cell microscopy is a powerful tool that can reveal cellular behavior as well as the underlying molecular processes. A key advantage of microscopy is that by visualizing biological processes, it can provide direct insights. Nevertheless, live-cell imaging can be technically challenging and prone to artifacts. For a successful experiment, many careful decisions are required at all steps from hardware selection to downstream image analysis. Facing these questions can be particularly intimidating due to the requirement for expertise in multiple disciplines, ranging from optics, biophysics, and programming to cell biology. In this review, we aim to summarize the key points that need to be considered when setting up and analyzing a live-cell imaging experiment. While we put a particular focus on yeast, many of the concepts discussed are applicable also to other organisms. In addition, we discuss reporting and data sharing strategies that we think are critical to improve reproducibility in the field.
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Affiliation(s)
| | - Fabian P. Schlottmann
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Jennifer C. Ewald
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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102
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Pócsi I, Szigeti ZM, Emri T, Boczonádi I, Vereb G, Szöllősi J. Use of red, far-red, and near-infrared light in imaging of yeasts and filamentous fungi. Appl Microbiol Biotechnol 2022; 106:3895-3912. [PMID: 35599256 PMCID: PMC9200671 DOI: 10.1007/s00253-022-11967-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Abstract While phototoxicity can be a useful therapeutic modality not only for eliminating malignant cells but also in treating fungal infections, mycologists aiming to observe morphological changes or molecular events in fungi, especially when long observation periods or high light fluxes are warranted, encounter problems owed to altered regulatory pathways or even cell death caused by various photosensing mechanisms. Consequently, the ever expanding repertoire of visible fluorescent protein toolboxes and high-resolution microscopy methods designed to investigate fungi in vitro and in vivo need to comply with an additional requirement: to decrease the unwanted side effects of illumination. In addition to optimizing exposure, an obvious solution is red-shifted illumination, which, however, does not come without compromises. This review summarizes the interactions of fungi with light and the various molecular biology and technology approaches developed for exploring their functions on the molecular, cellular, and in vivo microscopic levels, and outlines the progress towards reducing phototoxicity through applying far-red and near-infrared light. Key points • Fungal biological processes alter upon illumination, also under the microscope • Red shifted fluorescent protein toolboxes decrease interference by illumination • Innovations like two-photon, lightsheet, and near IR microscopy reduce phototoxicity
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Affiliation(s)
- István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
| | - Zsuzsa M Szigeti
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Imre Boczonádi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
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103
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Hajiabadi H, Mamontova I, Prizak R, Pancholi A, Koziolek A, Hilbert L. Deep-learning microscopy image reconstruction with quality control reveals second-scale rearrangements in RNA polymerase II clusters. PNAS NEXUS 2022; 1:pgac065. [PMID: 36741438 PMCID: PMC9896941 DOI: 10.1093/pnasnexus/pgac065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023]
Abstract
Fluorescence microscopy, a central tool of biological research, is subject to inherent trade-offs in experiment design. For instance, image acquisition speed can only be increased in exchange for a lowered signal quality, or for an increased rate of photo-damage to the specimen. Computational denoising can recover some loss of signal, extending the trade-off margin for high-speed imaging. Recently proposed denoising on the basis of neural networks shows exceptional performance but raises concerns of errors typical of neural networks. Here, we present a work-flow that supports an empirically optimized reduction of exposure times, as well as per-image quality control to exclude images with reconstruction errors. We implement this work-flow on the basis of the denoising tool Noise2Void and assess the molecular state and 3D shape of RNA polymerase II (Pol II) clusters in live zebrafish embryos. Image acquisition speed could be tripled, achieving 2-s time resolution and 350-nm lateral image resolution. The obtained data reveal stereotyped events of approximately 10 s duration: initially, the molecular mark for recruited Pol II increases, then the mark for active Pol II increases, and finally Pol II clusters take on a stretched and unfolded shape. An independent analysis based on fixed sample images reproduces this sequence of events, and suggests that they are related to the transient association of genes with Pol II clusters. Our work-flow consists of procedures that can be implemented on commercial fluorescence microscopes without any hardware or software modification, and should, therefore, be transferable to many other applications.
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Affiliation(s)
| | | | - Roshan Prizak
- Institute of Biological and Chemical Systems, Department of Biological Information Processing, Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany
| | - Agnieszka Pancholi
- Institute of Biological and Chemical Systems, Department of Biological Information Processing, Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany
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104
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Zeng Y, Cao R, Zhu J, Zhao W, Sun D, Zhang C. Continuous live cell imaging using dark field microscopy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1634-1637. [PMID: 35389402 DOI: 10.1039/d2ay00043a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The optical observation of live cell behavior is critical for biological and biomedical studies. The development of techniques for long-term cell and tissue imaging is, however, hindered by phototoxicity induced by excited fluorophores. We, herein, propose a methodology to capture live cell behavior using dark field microscopy (DM). Since the light intensity of DM is merely ∼0.1% of bright-field microscopy (BM) and ∼0.5% of fluorescence microscopy (FM), it allows super long and frequent live cell imaging. Our results demonstrate that continuous exposure to DM light for 48 h brings about no observable effect on the growth rate of 3T3 fibroblasts and HepG2 hepatoma cells, indicating minimum photo-toxicity. Moreover, DM images show contrast comparable to FM, which does not depend on the probes and staining efficiency. We, therefore, conclude that the proposed approach is suitable for long-term live cell imaging with super-high temporal resolution.
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Affiliation(s)
- Yang Zeng
- Address State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, 710127, China.
| | - Rui Cao
- Address State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, 710127, China.
| | - Jie Zhu
- Address State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, 710127, China.
| | - Wei Zhao
- Address State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, 710127, China.
| | - Dan Sun
- Address State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, 710127, China.
| | - Ce Zhang
- Address State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, 710127, China.
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105
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Talianov PM, Yakubova AA, Bukreeva A, Masharin M, Eliseev IE, Zelenkov L, Muslimov AR, Bukatin A, Gordeeva A, Kudryavtseva V, Makarov SV, Sukhorukov GB, Timin AS, Zyuzin MV. Incorporation of Perovskite Nanocrystals into Polymer Matrix for Enhanced Stability in Biological Media: In Vitro and In Vivo Studies. ACS APPLIED BIO MATERIALS 2022; 5:2411-2420. [PMID: 35426657 DOI: 10.1021/acsabm.2c00295] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The outstanding optical properties and multiphoton absorption of lead halide perovskites make them promising for use as fluorescence tags in bioimaging applications. However, their poor stability in aqueous media and biological fluids significantly limits their further use for in vitro and in vivo applications. In this work, we have developed a universal approach for the encapsulation of lead halide perovskite nanocrystals (PNCs) (CsPbBr3 and CsPbI3) as water-resistant fluorescent markers, which are suitable for fluorescence bioimaging. The obtained encapsulated PNCs demonstrate bright green emission at 510 nm (CsPbBr3) and red emission at 688 nm (CsPbI3) under one- and two-photon excitation, and they possess an enhanced stability in water and biological fluids (PBS, human serum) for a prolonged period of time (1 week). Further in vitro and in vivo experiments revealed enhanced stability of PNCs even after their introduction directly into the biological microenvironment (CT26 cells and DBA mice). The developed approach allows making a step toward stable, low-cost, and highly efficient bioimaging platforms that are spectrally tunable and have narrow emission.
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Affiliation(s)
- Pavel M Talianov
- School of Physics and Engineering, ITMO University, Lomonosova 9, 197101, St. Petersburg, Russian Federation
| | - Anastasia A Yakubova
- Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, St. Petersburg 195251, Russian Federation.,Laboratory of Renewable Energy Sources, Alferov University, Khlopin St. 8/3, St. Petersburg 194021, Russian Federation
| | - Anastasia Bukreeva
- Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, St. Petersburg 195251, Russian Federation
| | - Mikhail Masharin
- School of Physics and Engineering, ITMO University, Lomonosova 9, 197101, St. Petersburg, Russian Federation
| | - Igor E Eliseev
- Laboratory of Renewable Energy Sources, Alferov University, Khlopin St. 8/3, St. Petersburg 194021, Russian Federation
| | - Lev Zelenkov
- School of Physics and Engineering, ITMO University, Lomonosova 9, 197101, St. Petersburg, Russian Federation
| | - Albert R Muslimov
- Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, St. Petersburg 195251, Russian Federation.,Laboratory of Renewable Energy Sources, Alferov University, Khlopin St. 8/3, St. Petersburg 194021, Russian Federation
| | - Anton Bukatin
- Laboratory of Renewable Energy Sources, Alferov University, Khlopin St. 8/3, St. Petersburg 194021, Russian Federation
| | - Alexandra Gordeeva
- Skolkovo Institute of Science and Technology, Moscow 143026, Russian Federation
| | - Valeriya Kudryavtseva
- School of Engineering and Material Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Sergey V Makarov
- School of Physics and Engineering, ITMO University, Lomonosova 9, 197101, St. Petersburg, Russian Federation
| | - Gleb B Sukhorukov
- Skolkovo Institute of Science and Technology, Moscow 143026, Russian Federation.,School of Engineering and Material Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Alexander S Timin
- School of Physics and Engineering, ITMO University, Lomonosova 9, 197101, St. Petersburg, Russian Federation.,Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, St. Petersburg 195251, Russian Federation.,Research School of Chemical and Biomedical Engineering, National Research Tomsk Polytechnic University, Lenin Avenue 30, Tomsk 634050, Russia
| | - Mikhail V Zyuzin
- School of Physics and Engineering, ITMO University, Lomonosova 9, 197101, St. Petersburg, Russian Federation
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106
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Acuña-Rodriguez JP, Mena-Vega JP, Argüello-Miranda O. Live-cell fluorescence spectral imaging as a data science challenge. Biophys Rev 2022; 14:579-597. [PMID: 35528031 PMCID: PMC9043069 DOI: 10.1007/s12551-022-00941-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Live-cell fluorescence spectral imaging is an evolving modality of microscopy that uses specific properties of fluorophores, such as excitation or emission spectra, to detect multiple molecules and structures in intact cells. The main challenge of analyzing live-cell fluorescence spectral imaging data is the precise quantification of fluorescent molecules despite the weak signals and high noise found when imaging living cells under non-phototoxic conditions. Beyond the optimization of fluorophores and microscopy setups, quantifying multiple fluorophores requires algorithms that separate or unmix the contributions of the numerous fluorescent signals recorded at the single pixel level. This review aims to provide both the experimental scientist and the data analyst with a straightforward description of the evolution of spectral unmixing algorithms for fluorescence live-cell imaging. We show how the initial systems of linear equations used to determine the concentration of fluorophores in a pixel progressively evolved into matrix factorization, clustering, and deep learning approaches. We outline potential future trends on combining fluorescence spectral imaging with label-free detection methods, fluorescence lifetime imaging, and deep learning image analysis.
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Affiliation(s)
- Jessy Pamela Acuña-Rodriguez
- grid.412889.e0000 0004 1937 0706Center for Geophysical Research (CIGEFI), University of Costa Rica, San Pedro, San José Costa Rica
- grid.412889.e0000 0004 1937 0706School of Physics, University of Costa Rica, 2060 San Pedro, San José Costa Rica
| | - Jean Paul Mena-Vega
- grid.412889.e0000 0004 1937 0706School of Physics, University of Costa Rica, 2060 San Pedro, San José Costa Rica
| | - Orlando Argüello-Miranda
- grid.40803.3f0000 0001 2173 6074Department of Plant and Microbial Biology, North Carolina State University, 112 DERIEUX PLACE, Raleigh, NC 27695-7612 USA
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107
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Fisher CR, Ebeling MC, Ferrington DA. Quantification of mitophagy using mKeima-mito in cultured human primary retinal pigment epithelial cells. Exp Eye Res 2022; 217:108981. [PMID: 35167864 PMCID: PMC8957530 DOI: 10.1016/j.exer.2022.108981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/25/2022] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
The retinal pigment epithelium is a pigmented monolayer of cells that help maintain a healthy retina. Loss of this essential cell layer is implicated in a number of visual disorders, including age-related macular degeneration (AMD). Utilizing primary RPE cultures to investigate disease is an important step in understanding disease mechanisms. However, the use of primary RPE cultures presents a number of challenges, including the limited number of cells available and the presence of auto-fluorescent pigment that interferes with quantifying fluorescent probes. Additionally, primary RPE are difficult to transfect with exogenous nucleic acids traditionally used for fluorescent imaging. To overcome these challenges, we used an adeno-associated viral (AAV) vector to express a pH sensitive fluorescent protein, mKeima, fused to the mitochondrial targeting sequence of cytochrome oxidase subunit 8A (mKeima-mito). mKeima-mito allows for quantification of mitochondrial autophagy (mitophagy) in live-cell time-lapse imaging experiments. We also developed an image analysis pipeline to selectively quantify mKeima-mito while removing the signal of auto-fluorescent pigment from the dataset by utilizing information from the mKeima fluorescent channels. These techniques are demonstrated in primary RPE cultures expressing mKeima-mito treated with 2-[2-[4-(trifluoromethoxy)phenyl]hydrazinylidene]-propanedinitrile (FCCP), an uncoupler that depolarizes the mitochondrial membrane and leads to mitochondrial fragmentation and mitophagy. The techniques outlined provide a roadmap for investigating disease mechanisms or the effect of treatments utilizing fluorescent probes in an important cell culture model.
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Affiliation(s)
- Cody R Fisher
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, 55455, USA; Graduate Program in Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Mara C Ebeling
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Deborah A Ferrington
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, 55455, USA; Graduate Program in Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
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108
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Varnavski O, Gunthardt C, Rehman A, Luker GD, Goodson T. Quantum Light-Enhanced Two-Photon Imaging of Breast Cancer Cells. J Phys Chem Lett 2022; 13:2772-2781. [PMID: 35318850 DOI: 10.1021/acs.jpclett.2c00695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Correct biological interpretation from cell imaging can be achieved only if the observed phenomena proceed with negligible perturbation from the imaging system. Herein, we demonstrate microscopic images of breast cancer cells created by the fluorescence selectively excited in the process of entangled two-photon absorption in a scanning microscope at an excitation intensity orders of magnitude lower than that used for classical two-photon microscopy. Quantum enhanced entangled two-photon microscopy has shown cell imaging capabilities at an unprecedented low excitation intensity of ∼3.6 × 107 photons/s, which is a million times lower than the excitation level for the classical two-photon fluorescence image obtained in the same microscope. The extremely low light probe intensity demonstrated in entangled two-photon microscopy is of critical importance to minimize photobleaching during repetitive imaging and damage to cells in live-cell applications. This technology opens new avenues in cell investigations with light microscopy, such as enhanced selectivity and time-frequency resolution.
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109
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Mukunda DC, Rodrigues J, Joshi VK, Raghushaker CR, Mahato KK. A comprehensive review on LED-induced fluorescence in diagnostic pathology. Biosens Bioelectron 2022; 209:114230. [PMID: 35421670 DOI: 10.1016/j.bios.2022.114230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 03/19/2022] [Accepted: 03/25/2022] [Indexed: 11/02/2022]
Abstract
Sensitivity, specificity, mobility, and affordability are important criteria to consider for developing diagnostic instruments in common use. Fluorescence spectroscopy has been demonstrating substantial potential in the clinical diagnosis of diseases and evaluating the underlying causes of pathogenesis. A higher degree of device integration with appropriate sensitivity and reasonable cost would further boost the value of the fluorescence techniques in clinical diagnosis and aid in the reduction of healthcare expenses, which is a key economic concern in emerging markets. Light-emitting diodes (LEDs), which are inexpensive and smaller are attractive alternatives to conventional excitation sources in fluorescence spectroscopy, are gaining a lot of momentum in the development of affordable, compact analytical instruments of clinical relevance. The commercial availability of a broad range of LED wavelengths (255-4600 nm) has opened up new avenues for targeting a wide range of clinically significant molecules (both endogenous and exogenous), thereby diagnosing a range of clinical illnesses. As a result, we have specifically examined the uses of LED-induced fluorescence (LED-IF) in preclinical and clinical evaluations of pathological conditions, considering the present advancements in the field.
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Affiliation(s)
| | - Jackson Rodrigues
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
| | - Vijay Kumar Joshi
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
| | - Chandavalli Ramappa Raghushaker
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
| | - Krishna Kishore Mahato
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India.
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110
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Isokuortti J, Kiiski I, Sikanen T, Durandin N, Laaksonen T. Microfluidic oxygen tolerability screening of nanocarriers for triplet fusion photon upconversion. JOURNAL OF MATERIALS CHEMISTRY. C 2022; 10:4871-4877. [PMID: 35433006 PMCID: PMC8944590 DOI: 10.1039/d2tc00156j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/06/2022] [Indexed: 05/13/2023]
Abstract
The full potential of triplet fusion photon upconversion (TF-UC) of providing high-energy photons locally with low-energy excitation is limited in biomedicine and life sciences by its oxygen sensitivity. This hampers the applicability of TF-UC systems in sensors, imaging, optogenetics and drug release. Despite the advances in improving the oxygen tolerability of TF-UC systems, the evaluation of oxygen tolerability is based on comparing the performance at completely deoxygenated (0% oxygen) and ambient (20-21%) conditions, leaving the physiological oxygen levels (0.3-13.5%) neglected. This oversight is not deliberate and is only the result of the lack of simple and predictable methods to obtain and maintain these physiological oxygen levels in an optical setup. Herein, we demonstrate the use of microfluidic chips made of oxygen depleting materials to study the oxygen tolerability of four different micellar nanocarriers made of FDA-approved materials with various oxygen scavenging capabilities by screening their TF-UC performance over physiological oxygen levels. All nanocarriers were capable of efficient TF-UC even in ambient conditions. However, utilizing oxygen scavengers in the oil phase of the nanocarrier improves the oxygen tolerability considerably. For example, at the mean tumour oxygen level (1.4%), nanocarriers made of surfactants and oil phase both capable of oxygen scavenging retained remarkably 80% of their TF-UC emission. This microfluidic concept enables faster, simpler and more realistic evaluation of, not only TF-UC, but any micro or nanoscale oxygen-sensitive system and facilitates their development and implementation in biomedical and life science applications.
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Affiliation(s)
- Jussi Isokuortti
- Faculty of Engineering and Natural Sciences, Tampere University Tampere Finland
| | - Iiro Kiiski
- Faculty of Pharmacy, Drug Research Program, University of Helsinki Helsinki Finland
| | - Tiina Sikanen
- Faculty of Pharmacy, Drug Research Program, University of Helsinki Helsinki Finland
| | - Nikita Durandin
- Faculty of Engineering and Natural Sciences, Tampere University Tampere Finland
| | - Timo Laaksonen
- Faculty of Engineering and Natural Sciences, Tampere University Tampere Finland
- Faculty of Pharmacy, Drug Research Program, University of Helsinki Helsinki Finland
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111
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Fei K, Zhang J, Yuan J, Xiao P. Present Application and Perspectives of Organoid Imaging Technology. Bioengineering (Basel) 2022; 9:bioengineering9030121. [PMID: 35324810 PMCID: PMC8945799 DOI: 10.3390/bioengineering9030121] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/23/2022] [Accepted: 03/13/2022] [Indexed: 11/18/2022] Open
Abstract
An organoid is a miniaturized and simplified in vitro model with a similar structure and function to a real organ. In recent years, the use of organoids has increased explosively in the field of growth and development, disease simulation, drug screening, cell therapy, etc. In order to obtain necessary information, such as morphological structure, cell function and dynamic signals, it is necessary and important to directly monitor the culture process of organoids. Among different detection technologies, imaging technology is a simple and convenient choice and can realize direct observation and quantitative research. In this review, the principle, advantages and disadvantages of imaging technologies that have been applied in organoids research are introduced. We also offer an overview of prospective technologies for organoid imaging. This review aims to help biologists find appropriate imaging techniques for different areas of organoid research, and also contribute to the development of organoid imaging systems.
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112
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Reiche MA, Aaron JS, Boehm U, DeSantis MC, Hobson CM, Khuon S, Lee RM, Chew TL. When light meets biology - how the specimen affects quantitative microscopy. J Cell Sci 2022; 135:274812. [PMID: 35319069 DOI: 10.1242/jcs.259656] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fluorescence microscopy images should not be treated as perfect representations of biology. Many factors within the biospecimen itself can drastically affect quantitative microscopy data. Whereas some sample-specific considerations, such as photobleaching and autofluorescence, are more commonly discussed, a holistic discussion of sample-related issues (which includes less-routine topics such as quenching, scattering and biological anisotropy) is required to appropriately guide life scientists through the subtleties inherent to bioimaging. Here, we consider how the interplay between light and a sample can cause common experimental pitfalls and unanticipated errors when drawing biological conclusions. Although some of these discrepancies can be minimized or controlled for, others require more pragmatic considerations when interpreting image data. Ultimately, the power lies in the hands of the experimenter. The goal of this Review is therefore to survey how biological samples can skew quantification and interpretation of microscopy data. Furthermore, we offer a perspective on how to manage many of these potential pitfalls.
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Affiliation(s)
- Michael A Reiche
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Jesse S Aaron
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Ulrike Boehm
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Michael C DeSantis
- Light Microscopy Facility, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147,USA
| | - Chad M Hobson
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Satya Khuon
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA.,Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Rachel M Lee
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA.,Light Microscopy Facility, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147,USA
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113
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Campbell JM, Mahbub SB, Bertoldo MJ, Habibalahi A, Goss DM, Ledger WL, Gilchrist RB, Wu LE, Goldys EM. Multispectral autofluorescence characteristics of reproductive aging in old and young mouse oocytes. Biogerontology 2022; 23:237-249. [PMID: 35211812 PMCID: PMC9023381 DOI: 10.1007/s10522-022-09957-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/14/2022] [Indexed: 12/16/2022]
Abstract
Increasing age has a major detrimental impact on female fertility, which, with an ageing population, has major sociological implications. This impact is primarily mediated through deteriorating quality of the oocyte. Deteriorating oocyte quality with biological age is the greatest rate-limiting factor to female fertility. Here we have used label-free, non-invasive multi-spectral imaging to identify unique autofluorescence profiles of oocytes from young and aged animals. Discriminant analysis demonstrated that young oocytes have a distinct autofluorescent profile which accurately distinguishes them from aged oocytes. We recently showed that treatment with the nicotinamide adenine dinucleotide (NAD+) precursor nicotinamide mononucleotide (NMN) restored oocyte quality and fertility in aged animals, and when our analysis was applied to oocytes from aged animals treated with NMN, 85% of these oocytes were classified as having the autofluorescent signature of young animals. Spectral unmixing using the Robust Dependent Component Analysis (RoDECA) algorithm demonstrated that NMN treatment altered the metabolic profile of oocytes, increasing free NAD(P)H, protein bound NAD(P)H, redox ratio and the ratio of bound to free NAD(P)H. The frequency of oocytes with simultaneously high NAD(P)H and flavin content was also significantly increased in mice treated with NMN. Young and Aged + NMN oocytes had a smoother spectral distribution, with the distribution of NAD(P)H in young oocytes specifically differing from that of aged oocytes. Identifying the multispectral profile of oocyte autofluorescence during aging could have utility as a non-invasive and sensitive measure of oocyte quality.
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Affiliation(s)
- Jared M Campbell
- ARC Centre of Excellence Centre for Nanoscale Biophotonics, Graduate School of Biomedical Engineering, University of New South Wales Sydney, Kensington, Sydney, NSW, 2052, Australia.
| | - Saabah B Mahbub
- ARC Centre of Excellence Centre for Nanoscale Biophotonics, Graduate School of Biomedical Engineering, University of New South Wales Sydney, Kensington, Sydney, NSW, 2052, Australia
| | - Michael J Bertoldo
- Discipline of Women's Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, Australia
- School of Medical Sciences, University of New South Wales Sydney, Sydney, Australia
| | - Abbas Habibalahi
- ARC Centre of Excellence Centre for Nanoscale Biophotonics, Graduate School of Biomedical Engineering, University of New South Wales Sydney, Kensington, Sydney, NSW, 2052, Australia
| | - Dale M Goss
- School of Medical Sciences, University of New South Wales Sydney, Sydney, Australia
| | - William L Ledger
- Discipline of Women's Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, Australia
| | - Robert B Gilchrist
- Discipline of Women's Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, Australia
| | - Lindsay E Wu
- School of Medical Sciences, University of New South Wales Sydney, Sydney, Australia
| | - Ewa M Goldys
- ARC Centre of Excellence Centre for Nanoscale Biophotonics, Graduate School of Biomedical Engineering, University of New South Wales Sydney, Kensington, Sydney, NSW, 2052, Australia
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114
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Abstract
Cell manipulation in droplets has emerged as one of the great successes of microfluidic technologies, with the development of single-cell screening. However, the droplet format has also served to go beyond single-cell studies, namely by considering the interactions between different cells or between cells and their physical or chemical environment. These studies pose specific challenges linked to the need for long-term culture of adherent cells or the diverse types of measurements associated with complex biological phenomena. Here we review the emergence of droplet microfluidic methods for culturing cells and studying their interactions. We begin by characterizing the quantitative aspects that determine the ability to encapsulate cells, transport molecules, and provide sufficient nutrients within the droplets. This is followed by an evaluation of the biological constraints such as the control of the biochemical environment and promoting the anchorage of adherent cells. This first part ends with a description of measurement methods that have been developed. The second part of the manuscript focuses on applications of these technologies for cancer studies, immunology, and stem cells while paying special attention to the biological relevance of the cellular assays and providing guidelines on improving this relevance.
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Affiliation(s)
- Sébastien Sart
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.,Physical Microfluidics and Bioengineering, Institut Pasteur, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Gustave Ronteix
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.,Physical Microfluidics and Bioengineering, Institut Pasteur, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Shreyansh Jain
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.,Physical Microfluidics and Bioengineering, Institut Pasteur, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Gabriel Amselem
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.,Physical Microfluidics and Bioengineering, Institut Pasteur, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Charles N Baroud
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.,Physical Microfluidics and Bioengineering, Institut Pasteur, 25-28 Rue du Dr. Roux, 75015 Paris, France
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115
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Borah BJ, Sun CK. A rapid denoised contrast enhancement method digitally mimicking an adaptive illumination in submicron-resolution neuronal imaging. iScience 2022; 25:103773. [PMID: 35169684 PMCID: PMC8829796 DOI: 10.1016/j.isci.2022.103773] [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: 08/06/2021] [Revised: 12/07/2021] [Accepted: 01/12/2022] [Indexed: 12/02/2022] Open
Abstract
Optical neuronal imaging often shows ultrafine structures, such as a nerve fiber, coexisting with ultrabright structures, such as a soma with a substantially higher fluorescence-protein concentration. Owing to experimental and environmental factors, a laser-scanning multiphoton optical microscope (MPM) often encounters a high-frequency background noise that might contaminate such weak-intensity ultrafine neuronal structures. A straightforward contrast enhancement often leads to the saturation of the brighter ones, and might further amplify the high-frequency background noise. We report a digital approach called rapid denoised contrast enhancement (DCE), which digitally mimics a hardware-based adaptive/controlled illumination technique by means of digitally optimizing the signal strengths and hence the visibility of such weak-intensity structures while mostly preventing the saturation of the brightest ones. With large field-of-view (FOV) two-photon excitation fluorescence (TPEF) neuronal imaging, we validate the effectiveness of DCE over state-of-the-art digital image processing algorithms. With compute-unified-device-architecture (CUDA)-acceleration, a real-time DCE is further enabled with a reduced time complexity. A real-time applicable CUDA-accelerated Noise-suppressed Contrast Enhancement method Digitally mimics a traditional hardware-based adaptive/controlled illumination Drastically improves the visibility of noise-contaminated ultrafine neuronal structures Applicable in large-field high-NFOM multiphoton optical microscopes
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Affiliation(s)
- Bhaskar Jyoti Borah
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei 10617, Taiwan
| | - Chi-Kuang Sun
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei 10617, Taiwan.,Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan.,Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
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116
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Bioimaging approaches for quantification of individual cell behavior during cell fate decisions. Biochem Soc Trans 2022; 50:513-527. [PMID: 35166330 DOI: 10.1042/bst20210534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022]
Abstract
Tracking individual cells has allowed a new understanding of cellular behavior in human health and disease by adding a dynamic component to the already complex heterogeneity of single cells. Technically, despite countless advances, numerous experimental variables can affect data collection and interpretation and need to be considered. In this review, we discuss the main technical aspects and biological findings in the analysis of the behavior of individual cells. We discuss the most relevant contributions provided by these approaches in clinically relevant human conditions like embryo development, stem cells biology, inflammation, cancer and microbiology, along with the cellular mechanisms and molecular pathways underlying these conditions. We also discuss the key technical aspects to be considered when planning and performing experiments involving the analysis of individual cells over long periods. Despite the challenges in automatic detection, features extraction and long-term tracking that need to be tackled, the potential impact of single-cell bioimaging is enormous in understanding the pathogenesis and development of new therapies in human pathophysiology.
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117
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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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118
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Montgomery A, Garbouchian A, Bentley M. Visualizing Vesicle-Bound Kinesins in Cultured Hippocampal Neurons. Methods Mol Biol 2022; 2431:239-247. [PMID: 35412280 DOI: 10.1007/978-1-0716-1990-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Eukaryotic cells use microtubule-based vesicle transport to exchange molecules between compartments. Kinesin family members mediate all microtubule plus end-directed vesicle transport. Of the 45 kinesins expressed in humans, some 20 mediate microtubule plus-end directed vesicle transport. Here we describe a technique to visualize vesicle-bound kinesins in cultured hippocampal neurons. The method involves the expression of the vesicle-binding tail domain while minimizing the cytoplasmic pool. Using this approach drastically improves vesicle labeling compared to full-length kinesins. This tool is useful for systematically comparing the localization of different kinesins in the same cell type and for identifying cargo proteins that reside in vesicles moved by a specific kinesin family member. While we describe the assay in cultured hippocampal neurons, we expect it to be easily transferable to other eukaryotic cell types.
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Affiliation(s)
- Andrew Montgomery
- Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Alex Garbouchian
- Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Marvin Bentley
- Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.
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119
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Demuyser L, Van Genechten W, Van Dijck P. Assessment of cAMP-PKA Signaling in Candida glabrata by FRET-Based Biosensors. Methods Mol Biol 2022; 2542:177-191. [PMID: 36008665 DOI: 10.1007/978-1-0716-2549-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fluorescence or Förster resonance energy transfer (FRET)-based biosensors are used to monitor activity through molecular pathways inside the cell. Binding of secondary metabolites or enzyme-guided modification of protein targets can be assessed by quantifying the rate of energy transfer between two adequate fluorophores. The AKAR3 sensor contains a protein kinase A (PKA) phosphorylation site, which upon phosphorylation interacts with a ligand domain, bringing together FRET donor and acceptor fluorophores and allowing FRET. The EPAC2 sensor contains a cyclic adenosine monophosphate (cAMP)-binding domain. Upon binding of cAMP, donor and acceptor molecules are separated, thereby lowering energy transfer. Since the cAMP-PKA pathway is of great importance for regulation of growth, survival, and virulence in Candida species, monitoring the activity of this pathway in a time- and space-resolved manner allows for detailed investigation of potential drug targets. In this chapter, we describe how these FRET-based biosensors can be used in a practical setup.
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Affiliation(s)
- Liesbeth Demuyser
- VIB-KU Leuven Center for Microbiology, Flanders, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Heverlee, Leuven, Belgium
| | - Wouter Van Genechten
- VIB-KU Leuven Center for Microbiology, Flanders, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Heverlee, Leuven, Belgium
- Chemistry-Biochemistry Department, Molecular and Structural Biology Section, KU Leuven, Heverlee, Leuven, Belgium
| | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Flanders, Belgium.
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Heverlee, Leuven, Belgium.
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120
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Abstract
Live cell microscopy has become a common technique for exploring dynamic biological processes. When combined with fluorescent markers of cellular structures of interest, or fluorescent reporters of a biological activity of interest, live cell microscopy enables precise temporally and spatially resolved quantitation of the biological processes under investigation. However, because living cells are not normally exposed to light, live cell fluorescence imaging is significantly hindered by the effects of photodamage, which encompasses photobleaching of fluorophores and phototoxicity of the cells under observation. In this chapter, we outline several methods for optimizing and maintaining long-term imaging of live cells while simultaneously minimizing photodamage. This protocol demonstrates the intracellular trafficking of early and late endosomes following phagocytosis using both two and three dimensional imaging, but this protocol can easily be modified to image any biological process of interest in nearly any cell type.
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Affiliation(s)
- Alex Lac
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Austin Le Lam
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada.
- Robarts Research Institute, London, ON, Canada.
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121
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Dye NA. Cultivation and Live Imaging of Drosophila Imaginal Discs. Methods Mol Biol 2022; 2540:317-334. [PMID: 35980586 DOI: 10.1007/978-1-0716-2541-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this chapter, I present a method for the ex vivo cultivation and live imaging of Drosophila imaginal disc explants using low concentrations of the steroid hormone 20-hydroxyecdysone (20E). This method has been optimized for analyzing cellular dynamics during wing disc growth and leverages recent insights from in vivo experiments demonstrating that 20E is required for growth and patterning of the imaginal tissues. Using this protocol, we directly observe wing disc proliferation at a rapid rate for at least 13 h during live imaging. The orientation of tissue growth is also consistent with that inferred from indirect in vivo techniques. Thus, this method provides an improved way of studying dynamic cellular processes and tissue movements during imaginal disc development. I first describe the preparation of the growth medium and the dissection, and then I include a protocol for mounting and live imaging of the explants.
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Affiliation(s)
- Natalie A Dye
- Mildred Scheel Nachwuchszentrum (MSNZ) P2 & Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany.
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122
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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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123
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Chuyen A, Daian F, Pasini A, Kodjabachian L. A live-imaging protocol to track cell movement in the Xenopus embryo. STAR Protoc 2021; 2:100928. [PMID: 34778847 PMCID: PMC8577151 DOI: 10.1016/j.xpro.2021.100928] [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] [Indexed: 11/01/2022] Open
Abstract
Tracking individual cell movement during development is challenging, particularly in tissues subjected to major remodeling. Currently, most live imaging techniques in Xenopus are limited to tissue explants and/or to superficial cells. We describe here a protocol to track immature multiciliated cells (MCCs) moving within the inner epidermal layer of a whole embryo. In addition, we present a data processing protocol to uncouple the movements of individual cells from the coplanar drifts of the tissue in which they are embedded. For complete details on the use and execution of this protocol, please refer to Chuyen et al. (2021).
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Affiliation(s)
- Alexandre Chuyen
- Aix-Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Fabrice Daian
- Aix-Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Andrea Pasini
- Aix-Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Laurent Kodjabachian
- Aix-Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
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124
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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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125
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Niwa K, Hattori K, Fukuda D. Few-Photon Spectral Confocal Microscopy for Cell Imaging Using Superconducting Transition Edge Sensor. Front Bioeng Biotechnol 2021; 9:789709. [PMID: 34976979 PMCID: PMC8715037 DOI: 10.3389/fbioe.2021.789709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
A superconducting transition edge sensor (TES) is an energy-dispersive single-photon detector that distinguishes the wavelength of each incident photon from visible to near-infrared (NIR) without using spectral dispersive elements. Here, we introduce an application of the TES technique for confocal laser scanning microscopy (CLSM) as proof of our concept of ultra-sensitive and wide-band wavelength range color imaging for biological samples. As a reference sample for wide-band observation, a fixed fluorescence-labeled cell sample stained with three different color dyes was observed using our TES-based CLSM method. The three different dyes were simultaneously excited by irradiating 405 and 488 nm lasers, which were coupled using an optical fiber combiner. Even when irradiated at low powers of 80 and 120 nW with the 405 and 488 nm lasers respectively, emission signals were spectrally detected by the TES and categorized into four wavelength bands: up to 500 nm (blue), from 500 to 600 nm (green), from 600 to 800 nm (red), and from 800 to 1,200 nm (NIR). Using a single scan, an RGB color image and an NIR image of the fluorescent cell sample were successfully captured with tens of photon signals in a 40 ms exposure time for each pixel. This result demonstrates that TES is a useful wide-band spectral photon detector in the field of life sciences.
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Affiliation(s)
- Kazuki Niwa
- Research Institute for Physical Measurement, National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- *Correspondence: Kazuki Niwa,
| | - Kaori Hattori
- Research Institute for Physical Measurement, National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory, Kashiwa, Japan
| | - Daiji Fukuda
- Research Institute for Physical Measurement, National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory, Kashiwa, Japan
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126
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Montero Llopis P, Senft RA, Ross-Elliott TJ, Stephansky R, Keeley DP, Koshar P, Marqués G, Gao YS, Carlson BR, Pengo T, Sanders MA, Cameron LA, Itano MS. Best practices and tools for reporting reproducible fluorescence microscopy methods. Nat Methods 2021; 18:1463-1476. [PMID: 34099930 DOI: 10.1038/s41592-021-01156-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/15/2021] [Indexed: 02/04/2023]
Abstract
Although fluorescence microscopy is ubiquitous in biomedical research, microscopy methods reporting is inconsistent and perhaps undervalued. We emphasize the importance of appropriate microscopy methods reporting and seek to educate researchers about how microscopy metadata impact data interpretation. We provide comprehensive guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities. We aim to improve microscopy reporting, thus improving the quality, rigor and reproducibility of image-based science.
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Affiliation(s)
| | - Rebecca A Senft
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | | | | | - Daniel P Keeley
- Neuroscience Microscopy Core, University of North Carolina, Chapel Hill, NC, USA
| | - Preman Koshar
- Neuroscience Microscopy Core, University of North Carolina, Chapel Hill, NC, USA
| | - Guillermo Marqués
- University Imaging Centers and Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Ya-Sheng Gao
- Duke Light Microscopy Core Facility, Duke University, Durham, NC, USA
| | | | - Thomas Pengo
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, USA
| | - Mark A Sanders
- University Imaging Centers and Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Lisa A Cameron
- Duke Light Microscopy Core Facility, Duke University, Durham, NC, USA
| | - Michelle S Itano
- Neuroscience Microscopy Core, University of North Carolina, Chapel Hill, NC, USA
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127
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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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Zhang J, Peng X, Wu Y, Ren H, Sun J, Tong S, Liu T, Zhao Y, Wang S, Tang C, Chen L, Chen Z. Red‐ and Far‐Red‐Emitting Zinc Probes with Minimal Phototoxicity for Multiplexed Recording of Orchestrated Insulin Secretion. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Junwei Zhang
- College of Future Technology Institute of Molecular Medicine National Biomedical Imaging Center Beijing Key Laboratory of Cardiometabolic Molecular Medicine Peking University Beijing 100871 China
| | - Xiaohong Peng
- College of Future Technology Institute of Molecular Medicine National Biomedical Imaging Center Beijing Key Laboratory of Cardiometabolic Molecular Medicine Peking University Beijing 100871 China
- State Key Laboratory of Membrane Biology Peking University Beijing 100871 China
| | - Yunxiang Wu
- College of Future Technology Institute of Molecular Medicine National Biomedical Imaging Center Beijing Key Laboratory of Cardiometabolic Molecular Medicine Peking University Beijing 100871 China
| | - Huixia Ren
- Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
- Center for Quantitative Biology Peking University Beijing 100871 China
| | - Jingfu Sun
- PKU-Nanjing Institute of Translational Medicine Nanjing 211800 China
| | - Shiyan Tong
- School of Life Science Peking University Beijing 100871 China
| | - Tianyan Liu
- Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Yiwen Zhao
- College of Future Technology Institute of Molecular Medicine National Biomedical Imaging Center Beijing Key Laboratory of Cardiometabolic Molecular Medicine Peking University Beijing 100871 China
| | - Shusen Wang
- Organ Transplant Center Tianjin First Central Hospital Nankai University Tianjin 300192 China
| | - Chao Tang
- Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
- Center for Quantitative Biology Peking University Beijing 100871 China
| | - Liangyi Chen
- College of Future Technology Institute of Molecular Medicine National Biomedical Imaging Center Beijing Key Laboratory of Cardiometabolic Molecular Medicine Peking University Beijing 100871 China
- State Key Laboratory of Membrane Biology Peking University Beijing 100871 China
| | - Zhixing Chen
- College of Future Technology Institute of Molecular Medicine National Biomedical Imaging Center Beijing Key Laboratory of Cardiometabolic Molecular Medicine Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
- PKU-Nanjing Institute of Translational Medicine Nanjing 211800 China
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129
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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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130
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Saffi GT, Tang E, Mamand S, Inpanathan S, Fountain A, Salmena L, Botelho RJ. Reactive oxygen species prevent lysosome coalescence during PIKfyve inhibition. PLoS One 2021; 16:e0259313. [PMID: 34813622 PMCID: PMC8610251 DOI: 10.1371/journal.pone.0259313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/16/2021] [Indexed: 11/19/2022] Open
Abstract
Lysosomes are terminal, degradative organelles of the endosomal pathway that undergo repeated fusion-fission cycles with themselves, endosomes, phagosomes, and autophagosomes. Lysosome number and size depends on balanced fusion and fission rates. Thus, conditions that favour fusion over fission can reduce lysosome numbers while enlarging their size. Conversely, favouring fission over fusion may cause lysosome fragmentation and increase their numbers. PIKfyve is a phosphoinositide kinase that generates phosphatidylinositol-3,5-bisphosphate to modulate lysosomal functions. PIKfyve inhibition causes an increase in lysosome size and reduction in lysosome number, consistent with lysosome coalescence. This is thought to proceed through reduced lysosome reformation and/or fission after fusion with endosomes or other lysosomes. Previously, we observed that photo-damage during live-cell imaging prevented lysosome coalescence during PIKfyve inhibition. Thus, we postulated that lysosome fusion and/or fission dynamics are affected by reactive oxygen species (ROS). Here, we show that ROS generated by various independent mechanisms all impaired lysosome coalescence during PIKfyve inhibition and promoted lysosome fragmentation during PIKfyve re-activation. However, depending on the ROS species or mode of production, lysosome dynamics were affected distinctly. H2O2 impaired lysosome motility and reduced lysosome fusion with phagosomes, suggesting that H2O2 reduces lysosome fusogenecity. In comparison, inhibitors of oxidative phosphorylation, thiol groups, glutathione, or thioredoxin, did not impair lysosome motility but instead promoted clearance of actin puncta on lysosomes formed during PIKfyve inhibition. Additionally, actin depolymerizing agents prevented lysosome coalescence during PIKfyve inhibition. Thus, we discovered that ROS can generally prevent lysosome coalescence during PIKfyve inhibition using distinct mechanisms depending on the type of ROS.
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Affiliation(s)
- Golam T. Saffi
- Molecular Science Graduate Program, Ryerson University, Toronto, Ontario, Canada
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Evan Tang
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Sami Mamand
- Molecular Science Graduate Program, Ryerson University, Toronto, Ontario, Canada
- Polytechnic Research Center, Erbil Polytechnic University, Kurdistan Regional Government, Erbil, Kurdistan
| | - Subothan Inpanathan
- Molecular Science Graduate Program, Ryerson University, Toronto, Ontario, Canada
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Aaron Fountain
- Molecular Science Graduate Program, Ryerson University, Toronto, Ontario, Canada
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Leonardo Salmena
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Roberto J. Botelho
- Molecular Science Graduate Program, Ryerson University, Toronto, Ontario, Canada
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
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131
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Camphausen R, Cuevas Á, Duempelmann L, Terborg RA, Wajs E, Tisa S, Ruggeri A, Cusini I, Steinlechner F, Pruneri V. A quantum-enhanced wide-field phase imager. SCIENCE ADVANCES 2021; 7:eabj2155. [PMID: 34788099 PMCID: PMC8598016 DOI: 10.1126/sciadv.abj2155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Quantum techniques can be used to enhance the signal-to-noise ratio in optical imaging. Leveraging the latest advances in single-photon avalanche diode array cameras and multiphoton detection techniques, here, we introduce a supersensitive phase imager, which uses space-polarization hyperentanglement to operate over a large field of view without the need of scanning operation. We show quantum-enhanced imaging of birefringent and nonbirefringent phase samples over large areas, with sensitivity improvements over equivalent classical measurements carried out with equal number of photons. The potential applicability is demonstrated by imaging a biomedical protein microarray sample. Our technology is inherently scalable to high-resolution images and represents an essential step toward practical quantum-enhanced imaging.
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Affiliation(s)
- Robin Camphausen
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain
- Corresponding author. (R.C.); (Á.C.); (V.P.)
| | - Álvaro Cuevas
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain
- Corresponding author. (R.C.); (Á.C.); (V.P.)
| | - Luc Duempelmann
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain
| | - Roland A. Terborg
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain
| | - Ewelina Wajs
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain
| | - Simone Tisa
- Micro Photon Device SRL, Via Waltraud Gebert Deeg 3f, 39100 Bolzano, Italy
| | - Alessandro Ruggeri
- Micro Photon Device SRL, Via Waltraud Gebert Deeg 3f, 39100 Bolzano, Italy
| | - Iris Cusini
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Via Giuseppe Ponzio, 34, 20133 Milano, Italy
| | - Fabian Steinlechner
- Fraunhofer Institute for Applied Optics and Precision Engineering IOF, Albert-Einstein-Str. 7, 07745 Jena, Germany
- Abbe Center of Photonics, Friedrich Schiller University Jena, Albert-Einstein-Str. 6, 07745 Jena, Germany
| | - Valerio Pruneri
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain
- ICREA-Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010 Barcelona, Spain
- Corresponding author. (R.C.); (Á.C.); (V.P.)
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132
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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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133
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Li AC, Vyas S, Lin YH, Huang YY, Huang HM, Luo Y. Patch-Based U-Net Model for Isotropic Quantitative Differential Phase Contrast Imaging. IEEE TRANSACTIONS ON MEDICAL IMAGING 2021; 40:3229-3237. [PMID: 34152982 DOI: 10.1109/tmi.2021.3091207] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Quantitative differential phase-contrast (qDPC) imaging is a label-free phase retrieval method for weak phase objects using asymmetric illumination. However, qDPC imaging with fewer intensity measurements leads to anisotropic phase distribution in reconstructed images. In order to obtain isotropic phase transfer function, multiple measurements are required; thus, it is a time-consuming process. Here, we propose the feasibility of using deep learning (DL) method for isotropic qDPC microscopy from the least number of measurements. We utilize a commonly used convolutional neural network namely U-net architecture, trained to generate 12-axis isotropic reconstructed cell images (i.e. output) from 1-axis anisotropic cell images (i.e. input). To further extend the number of images for training, the U-net model is trained with a patch-wise approach. In this work, seven different types of living cell images were used for training, validation, and testing datasets. The results obtained from testing datasets show that our proposed DL-based method generates 1-axis qDPC images of similar accuracy to 12-axis measurements. The quantitative phase value in the region of interest is recovered from 66% up to 97%, compared to ground-truth values, providing solid evidence for improved phase uniformity, as well as retrieved missing spatial frequencies in 1-axis reconstructed images. In addition, results from our model are compared with paired and unpaired CycleGANs. Higher PSNR and SSIM values show the advantage of using the U-net model for isotropic qDPC microscopy. The proposed DL-based method may help in performing high-resolution quantitative studies for cell biology.
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134
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van der Leun AM, Hoekstra ME, Reinalda L, Scheele CLGJ, Toebes M, van de Graaff MJ, Chen LYY, Li H, Bercovich A, Lubling Y, David E, Thommen DS, Tanay A, van Rheenen J, Amit I, van Kasteren SI, Schumacher TN. Single-cell analysis of regions of interest (SCARI) using a photosensitive tag. Nat Chem Biol 2021; 17:1139-1147. [PMID: 34504322 PMCID: PMC7611907 DOI: 10.1038/s41589-021-00839-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/24/2021] [Indexed: 11/25/2022]
Abstract
The functional activity and differentiation potential of cells are determined by their interactions with surrounding cells. Approaches that allow unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by a tradeoff between spatial resolution and cell profiling depth. Here, we develop a photocage-based technology that allows isolation and in-depth analysis of live cells from regions of interest in complex ex vivo systems, including primary human tissues. The use of a highly sensitive 4-nitrophenyl(benzofuran) cage coupled to a set of nanobodies allows high-resolution photo-uncaging of different cell types in areas of interest. Single-cell RNA-sequencing of spatially defined CD8+ T cells is used to exemplify the feasibility of identifying location-dependent cell states. The technology described here provides a valuable tool for the analysis of spatially defined cells in diverse biological systems, including clinical samples.
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Affiliation(s)
- Anne M van der Leun
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mirjam E Hoekstra
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Luuk Reinalda
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Colinda L G J Scheele
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
- VIB-KULeuven Center for Cancer Biology, Leuven, Belgium
| | - Mireille Toebes
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Michel J van de Graaff
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
- SeraNovo, Leiden, Netherlands
| | - Linda Y Y Chen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Hanjie Li
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
- Shenzhen Institute of Synthetic Biology, Shenzhen, China
| | - Akhiad Bercovich
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Yaniv Lubling
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniela S Thommen
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Jacco van Rheenen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Sander I van Kasteren
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands.
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands.
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.
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135
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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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136
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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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137
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Drees C, Rühl P, Czerny J, Chandra G, Bajorath J, Haase M, Heinemann SH, Piehler J. Diffraction-Unlimited Photomanipulation at the Plasma Membrane via Specifically Targeted Upconversion Nanoparticles. NANO LETTERS 2021; 21:8025-8034. [PMID: 34519216 DOI: 10.1021/acs.nanolett.1c02267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Engineered UCNP are used to trigger rapid photoconversion of the fluorescent protein Dendra2 with nanoscopic precision and over longer distances in mammalian cells. By exploiting the synergy of high-level thulium doping with core-shell design and elevated excitation intensities, intense UCNP emission is achieved, allowing fast photoconversion of Dendra2 with <10 nm resolution. A tailored biocompatible surface coating and functionalization with a derivate of green fluorescent protein (GFP) for recognition of antiGFP nanobodies are developed. Highly specific targeting of UCNP to fusion proteins of antiGFP on the surface of mammalian cells is demonstrated. UCNP bound to extracellular Dendra2 enable rapid photoconversion selectively in molecular proximity and thus unambiguous detection of cytokine receptor dimerization in the plasma membrane and in endosomes. Remarkably, UCNPs are also suited for manipulating intracellular Dendra2 across the plasma membrane. This study thus establishes UCNP-controlled photomanipulation with nanoscale precision, opening exciting opportunities for bioanalytical applications in cell biology.
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Affiliation(s)
- Christoph Drees
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Philipp Rühl
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, 07745 Jena, Germany
| | - Jacqueline Czerny
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Gemini Chandra
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, 07745 Jena, Germany
| | - Janosch Bajorath
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Markus Haase
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Stefan H Heinemann
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, 07745 Jena, Germany
| | - Jacob Piehler
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
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138
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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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139
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Wolf S, Wan Y, McDole K. Current approaches to fate mapping and lineage tracing using image data. Development 2021; 148:dev198994. [PMID: 34498046 DOI: 10.1242/dev.198994] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Visualizing, tracking and reconstructing cell lineages in developing embryos has been an ongoing effort for well over a century. Recent advances in light microscopy, labelling strategies and computational methods to analyse complex image datasets have enabled detailed investigations into the fates of cells. Combined with powerful new advances in genomics and single-cell transcriptomics, the field of developmental biology is able to describe the formation of the embryo like never before. In this Review, we discuss some of the different strategies and applications to lineage tracing in live-imaging data and outline software methodologies that can be applied to various cell-tracking challenges.
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Affiliation(s)
- Steffen Wolf
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Yinan Wan
- Biozentrum, University of Basel, Basel, 4056, Switzerland
| | - Katie McDole
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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140
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Quantification of Myxococcus xanthus Aggregation and Rippling Behaviors: Deep-Learning Transformation of Phase-Contrast into Fluorescence Microscopy Images. Microorganisms 2021; 9:microorganisms9091954. [PMID: 34576849 PMCID: PMC8468851 DOI: 10.3390/microorganisms9091954] [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: 07/16/2021] [Revised: 08/25/2021] [Accepted: 08/31/2021] [Indexed: 11/17/2022] Open
Abstract
Myxococcus xanthus bacteria are a model system for understanding pattern formation and collective cell behaviors. When starving, cells aggregate into fruiting bodies to form metabolically inert spores. During predation, cells self-organize into traveling cell-density waves termed ripples. Both phase-contrast and fluorescence microscopy are used to observe these patterns but each has its limitations. Phase-contrast images have higher contrast, but the resulting image intensities lose their correlation with cell density. The intensities of fluorescence microscopy images, on the other hand, are well-correlated with cell density, enabling better segmentation of aggregates and better visualization of streaming patterns in between aggregates; however, fluorescence microscopy requires the engineering of cells to express fluorescent proteins and can be phototoxic to cells. To combine the advantages of both imaging methodologies, we develop a generative adversarial network that converts phase-contrast into synthesized fluorescent images. By including an additional histogram-equalized output to the state-of-the-art pix2pixHD algorithm, our model generates accurate images of aggregates and streams, enabling the estimation of aggregate positions and sizes, but with small shifts of their boundaries. Further training on ripple patterns enables accurate estimation of the rippling wavelength. Our methods are thus applicable for many other phenotypic behaviors and pattern formation studies.
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141
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Van Genechten W, Van Dijck P, Demuyser L. Fluorescent toys 'n' tools lighting the way in fungal research. FEMS Microbiol Rev 2021; 45:fuab013. [PMID: 33595628 PMCID: PMC8498796 DOI: 10.1093/femsre/fuab013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/14/2021] [Indexed: 12/13/2022] Open
Abstract
Although largely overlooked compared to bacterial infections, fungal infections pose a significant threat to the health of humans and other organisms. Many pathogenic fungi, especially Candida species, are extremely versatile and flexible in adapting to various host niches and stressful situations. This leads to high pathogenicity and increasing resistance to existing drugs. Due to the high level of conservation between fungi and mammalian cells, it is hard to find fungus-specific drug targets for novel therapy development. In this respect, it is vital to understand how these fungi function on a molecular, cellular as well as organismal level. Fluorescence imaging allows for detailed analysis of molecular mechanisms, cellular structures and interactions on different levels. In this manuscript, we provide researchers with an elaborate and contemporary overview of fluorescence techniques that can be used to study fungal pathogens. We focus on the available fluorescent labelling techniques and guide our readers through the different relevant applications of fluorescent imaging, from subcellular events to multispecies interactions and diagnostics. As well as cautioning researchers for potential challenges and obstacles, we offer hands-on tips and tricks for efficient experimentation and share our expert-view on future developments and possible improvements.
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Affiliation(s)
- Wouter Van Genechten
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200g, 3001 Leuven-Heverlee, Belgium
| | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
| | - Liesbeth Demuyser
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
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142
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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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143
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Verweij FJ, Balaj L, Boulanger CM, Carter DRF, Compeer EB, D'Angelo G, El Andaloussi S, Goetz JG, Gross JC, Hyenne V, Krämer-Albers EM, Lai CP, Loyer X, Marki A, Momma S, Nolte-'t Hoen ENM, Pegtel DM, Peinado H, Raposo G, Rilla K, Tahara H, Théry C, van Royen ME, Vandenbroucke RE, Wehman AM, Witwer K, Wu Z, Wubbolts R, van Niel G. The power of imaging to understand extracellular vesicle biology in vivo. Nat Methods 2021; 18:1013-1026. [PMID: 34446922 PMCID: PMC8796660 DOI: 10.1038/s41592-021-01206-3] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/20/2021] [Indexed: 01/08/2023]
Abstract
Extracellular vesicles (EVs) are nano-sized lipid bilayer vesicles released by virtually every cell type. EVs have diverse biological activities, ranging from roles in development and homeostasis to cancer progression, which has spurred the development of EVs as disease biomarkers and drug nanovehicles. Owing to the small size of EVs, however, most studies have relied on isolation and biochemical analysis of bulk EVs separated from biofluids. Although informative, these approaches do not capture the dynamics of EV release, biodistribution, and other contributions to pathophysiology. Recent advances in live and high-resolution microscopy techniques, combined with innovative EV labeling strategies and reporter systems, provide new tools to study EVs in vivo in their physiological environment and at the single-vesicle level. Here we critically review the latest advances and challenges in EV imaging, and identify urgent, outstanding questions in our quest to unravel EV biology and therapeutic applications.
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Affiliation(s)
- Frederik J Verweij
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France.
- GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France.
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - David R F Carter
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
- Evox Therapeutics Limited, Oxford Science Park, Oxford, UK
| | - Ewoud B Compeer
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Gisela D'Angelo
- Institut Curie, PSL Research University, CNRS, UMR144 Cell Biology and Cancer, Paris, France
| | - Samir El Andaloussi
- Evox Therapeutics Limited, Oxford Science Park, Oxford, UK
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jacky G Goetz
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Equipe Labellisée Ligue contre le Cancer, Strasbourg, France
| | | | - Vincent Hyenne
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Equipe Labellisée Ligue contre le Cancer, Strasbourg, France
- CNRS SNC5055, Strasbourg, France
| | - Eva-Maria Krämer-Albers
- Johannes Gutenberg-Universität Mainz, Institute of Developmental Biology and Neurobiology, Mainz, Germany
| | - Charles P Lai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Xavier Loyer
- Université de Paris, PARCC, INSERM, Paris, France
| | - Alex Marki
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Stefan Momma
- Institute of Neurology (Edinger Institute), Goethe-University, Frankfurt am Main, Germany
| | - Esther N M Nolte-'t Hoen
- Department of Biomolecular Health Sciences, Faculty of veterinary medicine, Utrecht University, Utrecht, the Netherlands
| | - D Michiel Pegtel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Hector Peinado
- Microenvironment and Metastasis Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR144 Cell Biology and Cancer, Paris, France
| | - Kirsi Rilla
- University of Eastern Finland, Institute of Biomedicine, Kuopio, Finland
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Clotilde Théry
- Institut Curie, PSL Research University, INSERM U932, Immunity and Cancer, Paris, France
| | | | - Roosmarijn E Vandenbroucke
- VIB Center for Inflammation Research and Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Ann M Wehman
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Kenneth Witwer
- Department of Molecular and Comparative Pathobiology and Neurology and the Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, China
- Medical School, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, China
| | - Richard Wubbolts
- Department of Biomolecular Health Sciences, Faculty of veterinary medicine, Utrecht University, Utrecht, the Netherlands
| | - Guillaume van Niel
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France.
- GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France.
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144
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Zhang J, Peng X, Wu Y, Ren H, Sun J, Tong S, Liu T, Zhao Y, Wang S, Tang C, Chen L, Chen Z. Red- and Far-Red-Emitting Zinc Probes with Minimal Phototoxicity for Multiplexed Recording of Orchestrated Insulin Secretion. Angew Chem Int Ed Engl 2021; 60:25846-25855. [PMID: 34423531 DOI: 10.1002/anie.202109510] [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] [Received: 07/16/2021] [Indexed: 11/12/2022]
Abstract
Zinc biology, featuring intertwining signaling networks and critical importance to human health, witnesses exciting opportunities in the big data era of physiology. Here, we report a class of red- and far-red-emitting Zn2+ probes with Kd values ranging from 190 nM to 74 μM, which are particularly suitable for real-time monitoring the high concentration of Zn2+ co-released with insulin during vesicular secretory events. Compared to the prototypical rhodamine-based Zn2+ probes, the new class exploits morpholino auxochromes which eliminates phototoxicity during long-term live recording of isolated islets. A Si-rhodamine-based Zn2+ probe with high turn-on ratio (>100), whose synthesis was enabled by a new route featuring late-stage N-alkylation, allowed simultaneous recording of Ca2+ influx, mitochondrial signal, and insulin secretion in isolated mouse islets. The time-lapse multicolor fluorescence movies and their analysis, enabled by red-shifted Zn2+ and other orthogonal physiological probes, highlight the potential impact of biocompatible fluorophores on the fields of islet endocrinology and system biology.
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Affiliation(s)
- Junwei Zhang
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871, China
| | - Xiaohong Peng
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871, China.,State Key Laboratory of Membrane Biology, Peking University, Beijing, 100871, China
| | - Yunxiang Wu
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871, China
| | - Huixia Ren
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Jingfu Sun
- PKU-Nanjing Institute of Translational Medicine, Nanjing, 211800, China
| | - Shiyan Tong
- School of Life Science, Peking University, Beijing, 100871, China
| | - Tianyan Liu
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China
| | - Yiwen Zhao
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871, China
| | - Shusen Wang
- Organ Transplant Center, Tianjin First Central Hospital, Nankai University, Tianjin, 300192, China
| | - Chao Tang
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Liangyi Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871, China.,State Key Laboratory of Membrane Biology, Peking University, Beijing, 100871, China
| | - Zhixing Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871, China.,Peking-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China.,PKU-Nanjing Institute of Translational Medicine, Nanjing, 211800, China
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145
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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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146
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Vasquez D, Knorr F, Hoffmann F, Ernst G, Marcu L, Schmitt M, Guntinas-Lichius O, Popp J, Schie IW. Multimodal Scanning Microscope Combining Optical Coherence Tomography, Raman Spectroscopy and Fluorescence Lifetime Microscopy for Mesoscale Label-Free Imaging of Tissue. Anal Chem 2021; 93:11479-11487. [PMID: 34380310 DOI: 10.1021/acs.analchem.1c01637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multimodal optical imaging of tissue has significant potential to become an indispensable diagnostic tool in clinical pathology. Conventional bright-field microscopy provides contrast based on attenuation or reflectance of light, having no depth-related information and no molecular specificity. Recent developments in biomedical optics have introduced a variety of optical modalities, such as Raman spectroscopy (RS), fluorescence lifetime imaging microscopy (FLIM) of endogenous fluorophores, optical coherence tomography (OCT), and others, which provide a distinct characteristic, i.e., molecular, chemical, and morphological information, of the sample. To harvest the full analytical potential of those modalities, we have developed a novel multimodal imaging system, which allows the co-registered acquisition of OCT/FLIM/RS on a single device. The present implementation allows the investigation of biological tissues in the mesoscale range, 0.1-5 mm in a correlated manner. Due to the co-registered acquisition of the modalities, it is possible to directly compare and evaluate the corresponding information between the three modalities. Moreover, by additionally preparing and characterizing entire pathological hematoxylin and eosin (H&E) slides of head and neck biopsies, it is also possible to correlate the multimodal spectroscopic information to any location of the ground truth H&E information. To the best of our knowledge, this is the first development and implementation of a compact and clinically applicable multimodal scanning microscope, which combines OCT, FLIM, and RS together with the possibility for co-registering H&E information for a morpho-chemical tissue characterization and a correlation with the pathological ground truth (H&E) of the underlying signal origin directly in a clinical environment.
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Affiliation(s)
- David Vasquez
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Florian Knorr
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Franziska Hoffmann
- Department of Otorhinolaryngology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
| | - Günther Ernst
- Department of Otorhinolaryngology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
| | - Laura Marcu
- Department of Biomedical Engineering, University of California Davis, One Shields Ave, Davis, California 95616, United States
| | - Michael Schmitt
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | | | - Jürgen Popp
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Iwan W Schie
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Department for Medical Engineering and Biotechnology, University of Applied Sciences-Jena, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
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147
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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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148
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Schibeci Natoli Scialli N, Colitti B, Bertolotti L, Pezzoni G, Martignani E, Melega M, Brocchi E, Rosati S. Genome editing of a hybridoma cell line via the CRISPR/Cas9 system: A new approach for constitutive high-level expression of heterologous proteins in eukaryotic system. Vet Immunol Immunopathol 2021; 238:110286. [PMID: 34171554 DOI: 10.1016/j.vetimm.2021.110286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 05/22/2021] [Accepted: 06/14/2021] [Indexed: 11/20/2022]
Abstract
The power of the CRISPR/Cas9 system has revolutionized genome editing in many fields of biology. These applications have expanded exponentially over recent years, including those regarding protein expression technologies. The CRISPR/Cas9 system avoids random integration of the gene of interest and due to this characteristic can be exploited to obtain a stable cell line for the high-yield expression of recombinant proteins. Here we propose a method to edit a hybridoma cell line for the constitutive expression of proteins of interest using the CRISPR/Cas9 system. First, with the scope of optimizing the method, we replaced part of the light chain of immunoglobulin with the Green Fluorescent Protein (GFP) gene, obtaining a precise knock-in in the hybridoma genome. We confirmed the expression and secretion of GFP into the culture medium via fluorimetric analysis, as well as correct genome editing by RNA sequencing. Then, using the same approach, we included the gene encoding a protein of diagnostic interest, the Bovine Herpesvirus 1 glycoprotein E, in the donor DNA. We obtained a stable clone able to secrete gE protein in fusion with GFP into the culture medium. This result was confirmed by ELISA and Western Blot analysis. This study confirms the suitability of this cell line for the production of proteins of diagnostic interest by stable gene expression in a mammalian system. These experiments will enable the technique to be developed from its proof of concept to more specific applications in the field of infectious disease diagnostics.
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Affiliation(s)
| | - Barbara Colitti
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Luigi Bertolotti
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Giulia Pezzoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via Bianchi 7, 25124, Brescia, Italy
| | - Eugenio Martignani
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Maverick Melega
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Emiliana Brocchi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via Bianchi 7, 25124, Brescia, Italy
| | - Sergio Rosati
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy.
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149
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Real-Time Analysis of Oxygen Gradient in Oocyte Respiration Using a High-Density Microelectrode Array. BIOSENSORS-BASEL 2021; 11:bios11080256. [PMID: 34436058 PMCID: PMC8393405 DOI: 10.3390/bios11080256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 02/05/2023]
Abstract
Physiological events related to oxygen concentration gradients provide valuable information to determine the state of metabolizing biological cells. The existing oxygen sensing methods (i.e., optical photoluminescence, magnetic resonance, and scanning electrochemical) are well-established and optimized for existing in vitro analyses. However, such methods also present various limitations in resolution, real-time sensing performance, complexity, and costs. An electrochemical imaging system with an integrated microelectrode array (MEA) would offer attractive means of measuring oxygen consumption rate (OCR) based on the cell’s two-dimensional (2D) oxygen concentration gradient. This paper presents an application of an electrochemical sensor platform with a custom-designed complementary-metal-oxide-semiconductor (CMOS)-based microchip and its Pt-coated surface MEA. The high-density MEA provides 16,064 individual electrochemical pixels that cover a 3.6 mm × 3.6 mm area. Utilizing the three-electrode configuration, the system is capable of imaging low oxygen concentration (18.3 µM, 0.58 mg/L, or 13.8 mmHg) at 27.5 µm spatial resolution and up to 4 Hz temporal resolution. In vitro oxygen imaging experiments were performed to analyze bovine cumulus-oocytes-complexes cells OCR and oxygen flux density. The integration of a microfluidic system allows proper bio-sample handling and delivery to the MEA surface for imaging. Finally, the imaging results are processed and presented as 2D heatmaps, representing the dissolved oxygen concentration in the immediate proximity of the MEA. This paper provides the results of real-time 2D imaging of OCR of live cells/tissues to gain spatial and temporal dynamics of target cell metabolism.
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150
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Simsek MF, Özbudak EM. A 3-D Tail Explant Culture to Study Vertebrate Segmentation in Zebrafish. J Vis Exp 2021. [PMID: 34279500 DOI: 10.3791/61981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Vertebrate embryos pattern their major body axis as repetitive somites, the precursors of vertebrae, muscle, and skin. Somites progressively segment from the presomitic mesoderm (PSM) as the tail end of the embryo elongates posteriorly. Somites form with regular periodicity and scale in size. Zebrafish is a popular model organism as it is genetically tractable and has transparent embryos that allow for live imaging. Nevertheless, during somitogenesis, fish embryos are wrapped around a large, rounding yolk. This geometry limits live imaging of PSM tissue in zebrafish embryos, particularly at higher resolutions that require a close objective working distance. Here, we present a flattened 3-D tissue culture method for live imaging of zebrafish tail explants. Tail explants mimic intact embryos by displaying a proportional slowdown of axis elongation and shortening of rostrocaudal somite lengths. We are further able to stall axis elongation speed through explant culture. This, for the first time, enables us to untangle the chemical input of signaling gradients from the mechanistic input of axial elongation. In future studies, this method can be combined with a microfluidic setup to allow time-controlled pharmaceutical perturbations or screening of vertebrate segmentation without any drug penetration concerns.
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Affiliation(s)
- M Fethullah Simsek
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center; Department of Genetics, Albert Einstein College of Medicine;
| | - Ertugrul M Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine; Department of Genetics, Albert Einstein College of Medicine
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