1
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Vertegel P, Milkin P, Murashko A, Parker M, Peranidze K, Emashova N, Minko S, Reukov V. Cell detachment: A review of techniques, challenges, and opportunities for advancing biomedical research and applications. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2025; 196:50-68. [PMID: 40023326 DOI: 10.1016/j.pbiomolbio.2025.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Revised: 02/24/2025] [Accepted: 02/25/2025] [Indexed: 03/04/2025]
Abstract
Culturing living cells outside the body is a complex process involving various techniques. Despite advances, harvesting cells remains challenging, especially in light of new emerging and scaled-up cell culture technologies. Enzymatic adherent cell harvesting is the most used and robust technology but can harm cells. Non-enzymatic detachment methods offer advantages but also present challenges. Thermo-responsive polymers require precise control of the molecular characteristics and thickness of the thermoresponsive films, which makes this method less robust and more expensive. This review highlights the importance of controlling harvested cell quality and its relationship to cell binding and detachment mechanisms. Many alternative methods have not been extensively analyzed, and their impact on cell quality beyond standard viability assays is not yet known. Developing robust cell harvesting methods for bioreactor microcarriers is a rapidly growing challenge as the cell manufacturing industry expands. Microcarriers with stimuli-responsive coatings face challenges similar to those observed for laboratory-scale cell dishes and bring an additional aspect of the need for microbead recycling consideration. All that together underlines the importance of the research in biomaterials and biotechnology for cell manufacturing.
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Wang G, Li L, Sorrells JE, Chen J, Tu H. Gentle Label-Free Nonlinear Optical Imaging Relaxes Linear-Absorption-Mediated Triplet. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e15648. [PMID: 40432535 DOI: 10.1002/advs.202415648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 04/26/2025] [Indexed: 05/29/2025]
Abstract
Sample health is critical for live-cell fluorescence microscopy and has promoted light-sheet microscopy that restricts its ultraviolet-visible excitation to one plane inside a 3D sample. It is thus intriguing that laser-scanning nonlinear optical microscopy, which similarly restricts its near-infrared excitation, has not broadly enabled gentle label-free molecular imaging. It is hypothesized that intense near-infrared excitation induces phototoxicity via linear absorption of intrinsic biomolecules with subsequent triplet buildup, rather than the commonly assumed mechanism of nonlinear absorption. Using a reproducible phototoxicity assay based on the time-lapse elevation of autofluorescence (hyper-fluorescence) from a homogeneous tissue model (chicken breast), strong evidence is provided supporting this hypothesis. The study justifies a simple imaging technique, e.g., rapidly scanned sub-80-fs excitation with full triplet-relaxation, to mitigate this ubiquitous linear-absorption-mediated phototoxicity independent of sample types. The corresponding label-free imaging can track freely moving C. elegans in real-time at an irradiance up to one-half of water optical breakdown.
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Affiliation(s)
- Geng Wang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Lianhuang Li
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou, 350007, China
| | - Janet E Sorrells
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jianxin Chen
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou, 350007, China
| | - Haohua Tu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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3
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Yavitt FM, Khang A, Bera K, McNally DL, Blatchley MR, Gallagher AP, Klein OD, Castillo-Azofeifa D, Dempsey PJ, Anseth KS. Engineered epithelial curvature controls Paneth cell localization in intestinal organoids. CELL BIOMATERIALS 2025; 1:100046. [PMID: 40270579 PMCID: PMC12013698 DOI: 10.1016/j.celbio.2025.100046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2025]
Abstract
The cellular organization within organoid models is important to regulate tissue specific function, yet few engineering approaches can control or direct cellular organization. Here, a photodegradable hydrogel is used to create softened regions that direct crypt formation within intestinal organoids, where the dimensions of the photosoftened regions generate predictable and defined crypt architectures. Guided by in vivo metrics of crypt morphology, this photopatterning method is used to control the width and length of in vitro organoid crypts, which ultimately defines the curvature of the epithelium. By tracking expression of differentiated Paneth cell markers in real-time, we show that epithelial curvature directs the localization of Paneth cells within engineered crypts, providing user-directed control over organoid functionality. We anticipate that our improved control over organoid architecture and thus Paneth cell localization will lead to more consistent in vitro organoid models for both mechanistic studies and translational applications.
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Affiliation(s)
- F. Max Yavitt
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Alex Khang
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Kaustav Bera
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Delaney L. McNally
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Michael R. Blatchley
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Aaron P. Gallagher
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, 90089, USA
- School of Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Ophir D. Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, 90089, USA
- Department of Pediatrics and Guerin Children’s, Cedars-Sinai Medical Center, Los Angeles, CA, 90505, USA
- Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - David Castillo-Azofeifa
- Department of Regenerative Medicine, Genentech, Inc., South San Francisco, California, 94080, USA
| | - Peter J. Dempsey
- Section of Developmental Biology, Department of Pediatrics, University of Colorado, Denver, CO, 80045, USA
| | - Kristi S. Anseth
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
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Rogalski M, Arcab P, Wdowiak E, Picazo-Bueno JÁ, Micó V, Józwik M, Trusiak M. Hybrid Iterating-Averaging Low Photon Budget Gabor Holographic Microscopy. ACS PHOTONICS 2025; 12:1771-1782. [PMID: 40255508 PMCID: PMC12007103 DOI: 10.1021/acsphotonics.4c01863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Revised: 12/13/2024] [Accepted: 12/16/2024] [Indexed: 04/22/2025]
Abstract
Achieving high-contrast, label-free imaging with minimal impact on live cell culture behavior remains a primary challenge in quantitative phase imaging (QPI). By enabling imaging under low illumination intensities (low photon budget, LPB), it is possible to minimize cell photostimulation, phototoxicity, and photodamage while supporting long-term and high-speed observations. However, LPB imaging introduces significant difficulties in QPI due to high levels of camera shot noise and quantification noise. Digital in-line holographic microscopy (DIHM) is a QPI technique known for its robustness against LPB data. However, simultaneous minimization of shot noise and inherent in DIHM twin image perturbation remains a critical challenge. In this study, we present the iterative Gabor averaging (IGA) algorithm, a novel approach that integrates iterative phase retrieval with frame averaging to effectively suppress both twin image disturbance and shot noise in multiframe DIHM. The IGA algorithm achieves this by leveraging an iterative process that reconstructs high-fidelity phase images while selectively averaging camera shot noise across frames. Our simulations demonstrate that IGA consistently outperforms conventional methods, achieving superior reconstruction accuracy, particularly under high-noise conditions. Experimental validations involving high-speed imaging of dynamic sperm cells and a static phase test target measurement under low illumination further confirmed IGA's efficacy. The algorithm also proved successful for optically thin samples, which often yield low signal-to-noise holograms even at high photon budgets. These advancements make IGA a powerful tool for photostimulation-free, high-speed imaging of dynamic biological samples and enhance the ability to image samples with extremely low optical thickness, potentially transforming biomedical and environmental applications in low-light settings.
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Affiliation(s)
- Mikolaj Rogalski
- Warsaw
University of Technology, Institute of Micromechanics and Photonics, 8 Sw. A. Boboli St., 02-525 Warsaw, Poland
| | - Piotr Arcab
- Warsaw
University of Technology, Institute of Micromechanics and Photonics, 8 Sw. A. Boboli St., 02-525 Warsaw, Poland
| | - Emilia Wdowiak
- Warsaw
University of Technology, Institute of Micromechanics and Photonics, 8 Sw. A. Boboli St., 02-525 Warsaw, Poland
| | - José Ángel Picazo-Bueno
- Departamento
de Óptica y Optometría y Ciencias de la Visión, Universidad de Valencia, C/Doctor Moliner 50, 46100 Burjassot, Spain
- Biomedical
Technology Center, University of Muenster, Mendelstr. 17, D-48149 Muenster, Germany
| | - Vicente Micó
- Departamento
de Óptica y Optometría y Ciencias de la Visión, Universidad de Valencia, C/Doctor Moliner 50, 46100 Burjassot, Spain
| | - Michal Józwik
- Warsaw
University of Technology, Institute of Micromechanics and Photonics, 8 Sw. A. Boboli St., 02-525 Warsaw, Poland
| | - Maciej Trusiak
- Warsaw
University of Technology, Institute of Micromechanics and Photonics, 8 Sw. A. Boboli St., 02-525 Warsaw, Poland
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Liu J, Zhang X, Zhao B, Ling H, Li Y, Sun K, Chen S, Zhang Y, Zhai T, Zhang Y, Li F, Liu Q. In Situ Monitoring of Membrane Protein Dynamics Using High-Throughput Red-Light-Activated Single-Molecule Tracking. ACS NANO 2025; 19:13466-13478. [PMID: 40153256 DOI: 10.1021/acsnano.5c03182] [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: 03/30/2025]
Abstract
Single-molecule tracking offers nanometer resolution for studying individual molecule dynamics but is often limited by sparse labeling to avoid signal overlap. We present Red-Light-Activated Single-molecule Tracking (RE-LAST) strategy to address this challenge utilizing a photoactivatable probe, SiR670. SiR670 combines traditional silicon rhodamine with a photocage called SO, quenching fluorescence via photoinduced electron transfer (PET). Red light triggers SiR670 excitation, generating singlet oxygen that oxidizes the SO cage, halting PET and restoring fluorescence. RE-LAST used red light for both activation and imaging, eliminating harmful UV exposure. This method enables high-throughput single-molecule tracking, achieving approximately 9 times more tracks than conventional methods and allowing detailed classification of CD56 membrane protein motion. Furthermore, in situ imaging of single live cells revealed the effects of triplet quencher and oxygen scavenging system (OSS) on membrane protein dynamics. While triplet quenchers like Trolox had minimal impact on protein movement patterns, OSS significantly accelerated protein movement and increased the proportion of mobile proteins. This approach provides a comprehensive method for investigating membrane protein dynamics in living cells, contributing to further developments in cellular and molecular biology.
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Affiliation(s)
- Jinyang Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institution, Fudan University, Shanghai 200438, China
| | - Xuebo Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institution, Fudan University, Shanghai 200438, China
| | - Bingjie Zhao
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institution, Fudan University, Shanghai 200438, China
| | - Huan Ling
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institution, Fudan University, Shanghai 200438, China
| | - Yanzhong Li
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institution, Fudan University, Shanghai 200438, China
| | - Kuangshi Sun
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institution, Fudan University, Shanghai 200438, China
| | - Song Chen
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institution, Fudan University, Shanghai 200438, China
| | - Yanxin Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institution, Fudan University, Shanghai 200438, China
| | - Tianli Zhai
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institution, Fudan University, Shanghai 200438, China
| | - Yunxiang Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institution, Fudan University, Shanghai 200438, China
| | - Fuyou Li
- Institute of Translational Medicine, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, P.R. China
| | - Qian Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institution, Fudan University, Shanghai 200438, China
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6
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Chaturvedi V, Kumari R, Sharma P, Pati AK. Diverse Fluorescent Probe Concepts for Detection and Monitoring of Reactive Oxygen Species. Chem Asian J 2025; 20:e202401524. [PMID: 39924450 PMCID: PMC11980770 DOI: 10.1002/asia.202401524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 01/14/2025] [Accepted: 02/06/2025] [Indexed: 02/11/2025]
Abstract
World-wide research on reactive oxygen species (ROS) continues to reveal new information about the role and impact of ROS on human health and disease. ROS are generated in live cells as a byproduct of aerobic metabolism. Physiological concentrations of cellular ROS are important for signaling and homeostasis, but excessive generation of ROS causes apoptotic and necrotic cell death and various health disorders. Fluorescence technology is a powerful tool to detect, monitor, and image cellular ROS. The present review provides an overview of diverse organic dye-based fluorescent probe concepts that involve modifications of traditional fluorescent dyes utilizing basic principles of dye chemistry and photophysics. Fluorescence responses of the probes and their specificity towards ROS are discussed through analyses of their photophysical and photochemical parameters. We also provide an outlook on future directions of ROS-responsive fluorescent dyes, which could enable the design and development of advanced probes for gaining deeper insights into redox biology.
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Affiliation(s)
- Vineeta Chaturvedi
- Department of ChemistryBirla Institute of Technology and Science PilaniPilaniRajasthan333031India
| | - Ritu Kumari
- Department of ChemistryBirla Institute of Technology and Science PilaniPilaniRajasthan333031India
| | - Prakriti Sharma
- Department of ChemistryBirla Institute of Technology and Science PilaniPilaniRajasthan333031India
| | - Avik K. Pati
- Department of ChemistryBirla Institute of Technology and Science PilaniPilaniRajasthan333031India
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7
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Stamatov R, Uzunova S, Kicheva Y, Karaboeva M, Blagoev T, Stoynov S. Supra-second tracking and live-cell karyotyping reveal principles of mitotic chromosome dynamics. Nat Cell Biol 2025; 27:654-667. [PMID: 40185948 PMCID: PMC11991918 DOI: 10.1038/s41556-025-01637-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/11/2025] [Indexed: 04/07/2025]
Abstract
Mitotic chromosome dynamics are essential for the three-dimensional organization of the genome during the cell cycle, but the spatiotemporal characteristics of this process remain unclear due to methodological challenges. While Hi-C methods capture interchromosomal contacts, they lack single-cell temporal dynamics, whereas microscopy struggles with bleaching and phototoxicity. Here, to overcome these limitations, we introduce Facilitated Segmentation and Tracking of Chromosomes in Mitosis Pipeline (FAST CHIMP), pairing time-lapse super-resolution microscopy with deep learning. FAST CHIMP tracked all human chromosomes with 8-s resolution from prophase to telophase, identified 15 out of 23 homologue pairs in single cells and compared chromosomal positioning between mother and daughter cells. It revealed a centrosome-motion-dependent flow that governs the mapping between chromosome locations at prophase and their metaphase plate position. In addition, FAST CHIMP measured supra-second dynamics of intra- and interchromosomal contacts. This tool adds a dynamic dimension to the study of chromatin behaviour in live cells, promising advances beyond the scope of existing methods.
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Affiliation(s)
- Rumen Stamatov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Sonya Uzunova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Yoana Kicheva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Karaboeva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Tavian Blagoev
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Stoyno Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
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8
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Frangos SM, Damrich S, Gueiber D, Sanchez CP, Wiedemann P, Schwarz US, Hamprecht FA, Lanzer M. Deep learning image analysis for continuous single-cell imaging of dynamic processes in Plasmodium falciparum-infected erythrocytes. Commun Biol 2025; 8:487. [PMID: 40133663 PMCID: PMC11937545 DOI: 10.1038/s42003-025-07894-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 03/06/2025] [Indexed: 03/27/2025] Open
Abstract
Continuous high-resolution imaging of the disease-mediating blood stages of the human malaria parasite Plasmodium falciparum faces challenges due to photosensitivity, small parasite size, and the anisotropy and large refractive index of host erythrocytes. Previous studies often relied on snapshot galleries from multiple cells, limiting the investigation of dynamic cellular processes. We present a workflow enabling continuous, single-cell monitoring of live parasites throughout the 48-hour intraerythrocytic life cycle with high spatial and temporal resolution. This approach integrates label-free, three-dimensional differential interference contrast and fluorescence imaging using an Airyscan microscope, automated cell segmentation through pre-trained deep-learning algorithms, and 3D rendering for visualization and time-resolved analyses. As a proof of concept, we applied this workflow to study knob-associated histidine-rich protein (KAHRP) export into the erythrocyte compartment and its clustering beneath the plasma membrane. Our methodology opens avenues for in-depth exploration of dynamic cellular processes in malaria parasites, providing a valuable tool for further investigations.
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Affiliation(s)
- Sophia M Frangos
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Infectious Diseases, Parasitology, Im Neuenheimer Feld 324, Heidelberg, Germany
| | - Sebastian Damrich
- Heidelberg University, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 205, Heidelberg, Germany
- Hertie Institute for AI in Brain Health, University of Tübingen, Otfried-Müller-Straße 25, Tübingen, Germany
| | - Daniele Gueiber
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Infectious Diseases, Parasitology, Im Neuenheimer Feld 324, Heidelberg, Germany
- University of Applied Sciences Mannheim, Institute of Molecular and Cell Biology, Paul-Wittsack-Strasse 10, Mannheim, Germany
| | - Cecilia P Sanchez
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Infectious Diseases, Parasitology, Im Neuenheimer Feld 324, Heidelberg, Germany
| | - Philipp Wiedemann
- University of Applied Sciences Mannheim, Institute of Molecular and Cell Biology, Paul-Wittsack-Strasse 10, Mannheim, Germany
| | - Ulrich S Schwarz
- Heidelberg University, BioQuant and Institute for Theoretical Physics, Philosophenweg 19, Heidelberg, Germany
| | - Fred A Hamprecht
- Heidelberg University, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 205, Heidelberg, Germany
| | - Michael Lanzer
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Infectious Diseases, Parasitology, Im Neuenheimer Feld 324, Heidelberg, Germany.
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9
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Streit M, Budiarta M, Jungblut M, Beliu G. Fluorescent labeling strategies for molecular bioimaging. BIOPHYSICAL REPORTS 2025; 5:100200. [PMID: 39947326 PMCID: PMC11914189 DOI: 10.1016/j.bpr.2025.100200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 01/28/2025] [Accepted: 02/06/2025] [Indexed: 03/16/2025]
Abstract
Super-resolution microscopy (SRM) has transformed biological imaging by circumventing the diffraction limit of light and enabling the visualization of cellular structures and processes at the molecular level. Central to the capabilities of SRM is fluorescent labeling, which ensures the precise attachment of fluorophores to biomolecules and has direct impact on the accuracy and resolution of imaging. Continuous innovation and optimization in fluorescent labeling are essential for the successful application of SRM in cutting-edge biological research. In this review, we discuss recent advances in fluorescent labeling strategies for molecular bioimaging, with a special focus on protein labeling. We compare different approaches, highlight technological breakthroughs, and address challenges such as linkage error and labeling density. By evaluating both established and emerging methods, we aim to guide researchers through all aspects that should be considered before opting for any labeling technique.
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Affiliation(s)
- Marcel Streit
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Made Budiarta
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Marvin Jungblut
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Gerti Beliu
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany.
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10
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Chen PHB, Li XL, Baskin JM. Synthetic Lipid Biology. Chem Rev 2025; 125:2502-2560. [PMID: 39805091 PMCID: PMC11969270 DOI: 10.1021/acs.chemrev.4c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2025]
Abstract
Cells contain thousands of different lipids. Their rapid and redundant metabolism, dynamic movement, and many interactions with other biomolecules have justly earned lipids a reputation as a vexing class of molecules to understand. Further, as the cell's hydrophobic metabolites, lipids assemble into supramolecular structures─most commonly bilayers, or membranes─from which they carry out myriad biological functions. Motivated by this daunting complexity, researchers across disciplines are bringing order to the seeming chaos of biological lipids and membranes. Here, we formalize these efforts as "synthetic lipid biology". Inspired by the idea, central to synthetic biology, that our abilities to understand and build biological systems are intimately connected, we organize studies and approaches across numerous fields to create, manipulate, and analyze lipids and biomembranes. These include construction of lipids and membranes from scratch using chemical and chemoenzymatic synthesis, editing of pre-existing membranes using optogenetics and protein engineering, detection of lipid metabolism and transport using bioorthogonal chemistry, and probing of lipid-protein interactions and membrane biophysical properties. What emerges is a portrait of an incipient field where chemists, biologists, physicists, and engineers work together in proximity─like lipids themselves─to build a clearer description of the properties, behaviors, and functions of lipids and membranes.
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Affiliation(s)
- Po-Hsun Brian Chen
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Xiang-Ling Li
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy M Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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11
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Hanauske T, Koretz CC, Jungenitz T, Roeper J, Drakew A, Deller T. Electrophysiologically calibrated optogenetic stimulation of dentate granule cells mitigates dendritic spine loss in denervated organotypic entorhino-hippocampal slice cultures. Sci Rep 2025; 15:4563. [PMID: 39915664 PMCID: PMC11802742 DOI: 10.1038/s41598-025-88536-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 01/29/2025] [Indexed: 02/09/2025] Open
Abstract
Organotypic slice cultures (OTCs) are versatile tools for studying long-term structure-function relationships of neurons within a defined network (e.g. hippocampus). We developed a method for repeated experimenter-controlled activation of hippocampal granule cells (GCs) in OTCs within the incubator. After several days of contact-free photonic stimulation, we were able to ameliorate entorhinal denervation-induced structural damage in GCs. To achieve this outcome, we had to calibrate the intensity and duration of optogenetic (light) pulses using whole-cell electrophysiological recordings and multi-cell calcium imaging. Our findings showed that ChR2-expressing cells generated action potentials (APs) or calcium transients in response to illumination but were otherwise functionally indistinguishable from non-transduced GCs within the same neural circuit. However, the threshold for AP firing in single GCs varied based on the stimulus light intensity and the expression levels of ChR2. This information allowed us to calibrate light intensity for chronic stimulations. Denervated GCs exhibited significant spine loss four days post-denervation, but this detrimental effect was mitigated when AP firing was induced at a physiological GC bursting rate. Phototoxic damage caused by chronic light exposure was significantly reduced if illuminated with longer wavelength and by adding antioxidants to the culture medium. Our study presents a versatile approach for concurrent non-invasive manipulation and observation of neural circuit activity and remodeling in vitro.
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Affiliation(s)
- Tijana Hanauske
- Institute for Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.
| | - Carolin Christina Koretz
- Institute for Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
- Institute for Neurophysiology, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Tassilo Jungenitz
- Institute for Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Jochen Roeper
- Institute for Neurophysiology, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Alexander Drakew
- Institute for Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Thomas Deller
- Institute for Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
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12
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Lu Y, Chen C, Li H, Zhao P, Zhao Y, Li B, Zhou W, Fan G, Guan D, Zheng Y. Visible light-responsive hydrogels for cellular dynamics and spatiotemporal viscoelastic regulation. Nat Commun 2025; 16:1365. [PMID: 39904989 PMCID: PMC11794891 DOI: 10.1038/s41467-024-54880-0] [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: 03/15/2024] [Accepted: 11/21/2024] [Indexed: 02/06/2025] Open
Abstract
Viscoelastic heterogeneity of matrices plays a pivotal role in cancer cell spreading, migration, and metastasis. However, the creation of viscoelastic platforms with spatial-temporal regulation is hindered by cytotoxicity and short regulation durations. Our research presents a dual mechanism for stress relaxation regulation- both intrinsic and responsive- by incorporating Schiff base bonds and a visible light-responsive thiuram disulfide (TDS) moiety into the hydrogel. Modifying base bonds facilitates a broad spectrum of intrinsic stress relaxation times. At the same time, incorporating the visible light-responsive TDS moiety endows the hydrogel with responsive viscoelastic properties. These properties are characterized by minimal cytotoxicity, spatial-temporal controllability, dose dependency, and reversibility. Utilizing this platform, we demonstrate that ovarian cancer cells exhibit contrasting behaviors in contraction and spreading when subjected to dynamic stress relaxation changes over various time periods. Additionally, we observed a "memory effect" in the cell's response to alterations in stress relaxation time. We can spatially direct cell migration through viscoelastic heterogeneity, achieved via photopatterning substrates and laser spots. This innovative approach provides a means to regulate the viscoelasticity of hydrogels across a wide range of timescales, thereby opening avenues for more advanced studies into how cells interpret and respond to spatiotemporal viscoelastic signals.
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Affiliation(s)
- Yan Lu
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, PR China
| | - Cheng Chen
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, PR China
| | - Hangyu Li
- State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, PR China
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, PR China
| | - Peng Zhao
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, PR China
| | - Yuanfeng Zhao
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, PR China
| | - Bohan Li
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, PR China
| | - Wei Zhou
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, PR China
| | - Gaofeng Fan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, PR China
| | - Dongshi Guan
- State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, PR China.
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, PR China.
| | - Yijun Zheng
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, PR China.
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13
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Byrdin M, Byrdina S. Impact of triplet state population on GFP-type fluorescence and photobleaching. Biol Cell 2025; 117:e2400076. [PMID: 39945540 PMCID: PMC11823621 DOI: 10.1111/boc.202400076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 12/12/2024] [Accepted: 01/17/2025] [Indexed: 02/16/2025]
Abstract
BACKGROUND INFORMATION Based on recently published parameters (Rane et al. 2023, JPCB 127, 5046-5054) for (rs)EGFP triplet state formation and decay rates and yields, we consider the power density dependence of triplet state population dynamics and its consequences for the application of green fluorescent proteins in biological single molecule fluorescence microscopy. RESULTS We find that under certain conditions, the photon budget of GFP type fluorescent proteins can be linearly dependent on power density and we propose a possible explanation for such a non-Hirschfeld photobleaching behavior. Moreover, illumination with millisecond pulses at sub-kHz rates is shown to improve photostability. CONCLUSIONS We stipulate that a judicious choice of excitation wavelength should take into account the triplet state absorption spectrum along with the singlet state absorption spectrum. Formulas are given for the estimation of the effects of such choice as function of the experimental parameters. SIGNIFICANCE The linear photobleaching model as proposed by Hirschfeld 50 years ago with power-independent photon budget is not generally applicable to fluorescent proteins with millisecond-lived triplet states.
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Affiliation(s)
- Martin Byrdin
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBSGrenobleFrance
| | - Svetlana Byrdina
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, IRD, Univ. Gustave Eiffel, ISTerreGrenobleFrance
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14
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Zhou LM, Sun W, Tao ZQ, Xiong NJ, Huang C, Jiang XY, Ren YX, Yang Y, Shi YZ, Hu JG, Zhan Q. Subwavelength-scale off-axis optical nanomanipulation within Gaussian-beam traps. NANOPHOTONICS (BERLIN, GERMANY) 2025; 14:219-228. [PMID: 39927206 PMCID: PMC11806509 DOI: 10.1515/nanoph-2024-0527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Accepted: 12/19/2024] [Indexed: 02/11/2025]
Abstract
It is generally recognized that there is only a single optical potential-well near the focus in optical traps with a focused Gaussian beam. In this work, we show that this classic Gaussian-beam optical trap has additional optical potential-wells for optical manipulation at the subwavelength scale in the off-focus transverse plane. The additional optical potential-wells are formed by the synergy of both the gradient trapping force and the transverse scattering force, though in previous studies the scattering force usually has adverse effect such as reducing trapping stability. These potential-wells work for not only the metallic particles, but also the high refractive-index dielectric particles. By engineering the contribution of the gradient force and scattering force through the particle size, the particle material and the position of the manipulation transverse plane, the force field and trapping potential-well can be tailored to trap/manipulate nanoparticles at different off-axis distance at the subwavelength scale. Our work provides new insight into optical tweezers and promises applications in optical nanomanipulation, nanoparticle sorting/separation, particle patterning and micro-fabrication on substrates.
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Affiliation(s)
- Lei-Ming Zhou
- Department of Optical Engineering, School of Physics, Hefei University of Technology, Hefei, Anhui230601, China
| | - Wan Sun
- Department of Optical Engineering, School of Physics, Hefei University of Technology, Hefei, Anhui230601, China
| | - Zong-Qiang Tao
- Department of Optical Engineering, School of Physics, Hefei University of Technology, Hefei, Anhui230601, China
| | - Ning-Jun Xiong
- Department of Optical Engineering, School of Physics, Hefei University of Technology, Hefei, Anhui230601, China
| | - Chan Huang
- Department of Optical Engineering, School of Physics, Hefei University of Technology, Hefei, Anhui230601, China
| | - Xiao-Yun Jiang
- Department of Optical Engineering, School of Physics, Hefei University of Technology, Hefei, Anhui230601, China
| | - Yu-Xuan Ren
- Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
- Department of Neurology, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Yuanjie Yang
- School of Physics, University of Electronic Science and Technology of China, Chengdu611731, China
| | - Yu-Zhi Shi
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai200092, China
| | - Ji-Gang Hu
- Department of Optical Engineering, School of Physics, Hefei University of Technology, Hefei, Anhui230601, China
| | - Qiwen Zhan
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai200093, China
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15
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Li J, Zhu Z, Xue Y, Downes A. Analysis of Drug Molecules in Living Cells. Crit Rev Anal Chem 2025:1-16. [PMID: 39854220 DOI: 10.1080/10408347.2025.2453431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2025]
Abstract
Cells are the fundamental units of life, comprising a highly concentrated and complex assembly of biomolecules that interact dynamic ally across spatial and temporal scales. Living cells are constantly undergoing dynamic processes, therefore, to understand the interactions between drug molecules and living cells is of paramount importance in the biomedical sciences and pharmaceutical development. Compared with traditional end-point assays and fixed cell analysis, analysis of drug molecules in living cells can provide more insight into the effects of drugs on cells in real-time and allowing for a better understanding of drug mechanisms and effects, which will contribute to the development of drug developing and testing and personalize medicine. However, the high demands of living cell analysis, including high costs, technical complexity, and throughput limitations, hinder the widespread application of this technology. In recent years, the rapid development of analytical methods such as Raman spectroscopy and fluorescence has made the in situ and real-time detection possible, allowing the analysis of single cell or cell populations at various conditions. In this review, we summarize the advanced analytical methods and technologies from last few years for drug detection in living cells.
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Affiliation(s)
- Jiaming Li
- Department of Bioengineering, Faculty of Engineering, The University of Edinburgh, Edinburgh, UK
| | - Zhiyuan Zhu
- Department of Infection Medicine, Faculty of Medicine, The University of Edinburgh, Edinburgh, UK
| | - Yuxiang Xue
- Department of Bioengineering, Faculty of Engineering, The University of Edinburgh, Edinburgh, UK
| | - Andrew Downes
- Department of Bioengineering, Faculty of Engineering, The University of Edinburgh, Edinburgh, UK
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16
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Tan YY, Liu J, Su QP. Advancing Platelet Research Through Live-Cell Imaging: Challenges, Techniques, and Insights. SENSORS (BASEL, SWITZERLAND) 2025; 25:491. [PMID: 39860861 PMCID: PMC11768609 DOI: 10.3390/s25020491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 01/09/2025] [Accepted: 01/14/2025] [Indexed: 01/27/2025]
Abstract
Platelet cells are essential to maintain haemostasis and play a critical role in thrombosis. They swiftly respond to vascular injury by adhering to damaged vessel surfaces, activating signalling pathways, and aggregating with each other to control bleeding. This dynamic process of platelet activation is intricately coordinated, spanning from membrane receptor maturation to intracellular interactions to whole-cell responses. Live-cell imaging has become an invaluable tool for dissecting these complexes. Despite its benefits, live imaging of platelets presents significant technical challenges. This review addresses these challenges, identifying key areas in need of further development and proposing possible solutions. We also focus on the dynamic processes of platelet adhesion, activation, and aggregation in haemostasis and thrombosis, applying imaging capacities from the microscale to the nanoscale. By exploring various live imaging techniques, we demonstrate how these approaches offer crucial insights into platelet biology and deepen our understanding of these three core events. In conclusion, this review provides an overview of the imaging methods currently available for studying platelet dynamics, guiding researchers in selecting suitable techniques for specific studies. By advancing our knowledge of platelet behaviour, these imaging methods contribute to research on haemostasis, thrombosis, and platelet-related diseases, ultimately aiming to improve clinical outcomes.
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Affiliation(s)
- Yuping Yolanda Tan
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (Y.Y.T.); (J.L.)
- Heart Research Institute, Newtown, NSW 2042, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jinghan Liu
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (Y.Y.T.); (J.L.)
- Heart Research Institute, Newtown, NSW 2042, Australia
| | - Qian Peter Su
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (Y.Y.T.); (J.L.)
- Heart Research Institute, Newtown, NSW 2042, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW 2006, Australia
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17
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Vargas-Ordaz E, Newman H, Austin C, Catt S, Nosrati R, Cadarso VJ, Neild A, Horta F. Novel application of metabolic imaging of early embryos using a light-sheet on-a-chip device: a proof-of-concept study. Hum Reprod 2025; 40:41-55. [PMID: 39521726 PMCID: PMC11700888 DOI: 10.1093/humrep/deae249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/23/2024] [Indexed: 11/16/2024] Open
Abstract
STUDY QUESTION Is it feasible to safely determine metabolic imaging signatures of nicotinamide adenine dinucleotide [NAD(P)H] associated auto-fluorescence in early embryos using a light-sheet on-a-chip approach? SUMMARY ANSWER We developed an optofluidic device capable of obtaining high-resolution 3D images of the NAD(P)H autofluorescence of live mouse embryos using a light-sheet on-a-chip device as a proof-of-concept. WHAT IS KNOWN ALREADY Selecting the most suitable embryos for implantation and subsequent healthy live birth is crucial to the success rate of assisted reproduction and offspring health. Besides morphological evaluation using optical microscopy, a promising alternative is the non-invasive imaging of live embryos to establish metabolic activity performance. Indeed, in recent years, metabolic imaging has been investigated using highly advanced microscopy technologies such as fluorescence-lifetime imaging and hyperspectral microscopy. STUDY DESIGN, SIZE, DURATION The potential safety of the system was investigated by assessing the development and viability of live embryos after embryo culture for 67 h post metabolic imaging at the two-cell embryo stage (n = 115), including a control for culture conditions and sham controls (system non-illuminated). Embryo quality of developed blastocysts was assessed by immunocytochemistry to quantify trophectoderm and inner mass cells (n = 75). Furthermore, inhibition of metabolic activity (FK866 inhibitor) during embryo culture was also assessed (n = 18). PARTICIPANTS/MATERIALS, SETTING, METHODS The microstructures were fabricated following a standard UV-photolithography process integrating light-sheet fluorescence microscopy into a microfluidic system, including on-chip micro-lenses to generate a light-sheet at the centre of a microchannel. Super-ovulated F1 (CBA/C57Bl6) mice were used to produce two-cell embryos and embryo culture experiments. Blastocyst formation rates and embryo quality (immunocytochemistry) were compared between the study groups. A convolutional neural network (ResNet 34) model using metabolic images was also trained. MAIN RESULTS AND THE ROLE OF CHANCE The optofluidic device was capable of obtaining high-resolution 3D images of live mouse embryos that can be linked to their metabolic activity. The system's design allowed continuous tracking of the embryo location, including high control displacement through the light-sheet and fast imaging of the embryos (<2 s), while keeping a low dose of light exposure (16 J · cm-2 and 8 J · cm-2). Optimum settings for keeping sample viability showed that a modest light dosage was capable of obtaining 30 times higher signal-noise-ratio images than images obtained with a confocal system (P < 0.00001; t-test). The results showed no significant differences between the control, illuminated and non-illuminated embryos (sham control) for embryo development as well as embryo quality at the blastocyst stage (P > 0.05; Yate's chi-squared test). Additionally, embryos with inhibited metabolic activity showed a decreased blastocyst formation rate of 22.2% compared to controls, as well as a 47% reduction in metabolic activity measured by metabolic imaging (P < 0.0001; t-test). This indicates that the optofluidic device was capable of producing metabolic images of live embryos by measuring NAD(P)H autofluorescence, allowing a novel and affordable approach. The obtained metabolic images of two-cell embryos predicted blastocyst formation with an AUC of 0.974. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION The study was conducted using a mouse model focused on early embryo development assessing illumination at the two-cell stage. Further safety studies are required to assess the safety and use of 405 nm light at the blastocyst stage by investigating any potential negative impact on live birth rates, offspring health, aneuploidy rates, mutational load, changes in gene expression, and/or effects on epigenome stability in newborns. WIDER IMPLICATIONS OF THE FINDINGS This light-sheet on-a-chip approach is novel and after rigorous safety studies and a roadmap for technology development, potential future applications could be developed for ART. The overall cost-efficient fabrication of the device will facilitate scalability and integration into future devices if full-safety application is demonstrated. STUDY FUNDING/COMPETING INTEREST(S) This work was partially supported by an Ideas Grant (no 2004126) from the National Health and Medical Research Council (NHMRC), by the Education Program in Reproduction and Development (EPRD), Department Obstetrics and Gynaecology, Monash University, and by the Department of Mechanical and Aerospace Engineering, Faculty of Engineering, Monash University. The authors E.V-O, R.N., V.J.C., A.N., and F.H. have applied for a patent on the topic of this technology (PCT/AU2023/051132). The remaining authors have nothing to disclose.
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Affiliation(s)
- E Vargas-Ordaz
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC, Australia
- Centre to Impact Antimicrobial Resistance—Sustainable Solutions, Monash University, Clayton, VIC, Australia
| | - H Newman
- Education Program in Reproduction and Development, EPRD, Department of obstetrics and Gynaecology, Monash University, Clayton, VIC, Australia
| | - C Austin
- Education Program in Reproduction and Development, EPRD, Department of obstetrics and Gynaecology, Monash University, Clayton, VIC, Australia
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - S Catt
- Education Program in Reproduction and Development, EPRD, Department of obstetrics and Gynaecology, Monash University, Clayton, VIC, Australia
| | - R Nosrati
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC, Australia
| | - V J Cadarso
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC, Australia
- Centre to Impact Antimicrobial Resistance—Sustainable Solutions, Monash University, Clayton, VIC, Australia
| | - A Neild
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC, Australia
| | - F Horta
- Education Program in Reproduction and Development, EPRD, Department of obstetrics and Gynaecology, Monash University, Clayton, VIC, Australia
- Monash Data Future Institute, Monash University, Clayton, VIC, Australia
- Fertility & Research Center, Discipline of Women’s Health, Royal Hospital for Women & School of Clinical Medicine, The University of New South Wales, UNSW, Randwick, NSW, Australia
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18
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Bouvet P, Bevilacqua C, Ambekar Y, Antonacci G, Au J, Caponi S, Chagnon-Lessard S, Czarske J, Dehoux T, Fioretto D, Fu Y, Guck J, Hamann T, Heinemann D, Jähnke T, Jean-Ruel H, Kabakova I, Koski K, Koukourakis N, Krause D, La Cavera S, Landes T, Li J, Margueritat J, Mattarelli M, Monaghan M, Overby DR, Perez-Cota F, Pontecorvo E, Prevedel R, Ruocco G, Sandercock J, Scarcelli G, Scarponi F, Testi C, Török P, Vovard L, Weninger W, Yakovlev V, Yun SH, Zhang J, Palombo F, Bilenca A, Elsayad K. Consensus Statement on Brillouin Light Scattering Microscopy of Biological Materials. ARXIV 2024:arXiv:2411.11712v1. [PMID: 39606723 PMCID: PMC11601801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Brillouin Light Scattering (BLS) spectroscopy is a non-invasive, non-contact, label-free optical technique that can provide information on the mechanical properties of a material on the sub-micron scale. Over the last decade it has seen increased applications in the life sciences, driven by the observed significance of mechanical properties in biological processes, the realization of more sensitive BLS spectrometers and its extension to an imaging modality. As with other spectroscopic techniques, BLS measurements not only detect signals characteristic of the investigated sample, but also of the experimental apparatus, and can be significantly affected by measurement conditions. The aim of this consensus statement is to improve the comparability of BLS studies by providing reporting recommendations for the measured parameters and detailing common artifacts. Given that most BLS studies of biological matter are still at proof-of-concept stages and use different--often self-built--spectrometers, a consensus statement is particularly timely to assure unified advancement.
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Affiliation(s)
- Pierre Bouvet
- Center for Anatomy and Cell Biology, Medical University of Vienna, Austria
| | - Carlo Bevilacqua
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Germany
| | | | | | - Joshua Au
- Fischell Department of Bioengineering, University of Maryland, USA
| | - Silvia Caponi
- CNR - Istituto Officina dei Materiali (IOM), Unità di Perugia, Italy
| | | | - Juergen Czarske
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Germany
- Competence Center for Biomedical Computational Laser Systems, TU Dresden, Germany
| | - Thomas Dehoux
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, France
| | | | - Yujian Fu
- Center for Anatomy and Cell Biology, Medical University of Vienna, Austria
| | - Jochen Guck
- Max Planck Institute for the Science of Light, Erlangen, Germany
| | - Thorsten Hamann
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Dag Heinemann
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Germany
| | | | | | - Irina Kabakova
- School of Mathematical and Physical Sciences, University of Technology Sydney, Australia
| | - Kristie Koski
- Department of Chemistry, University of California Davis, USA
| | - Nektarios Koukourakis
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Germany
| | - David Krause
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Germany
| | - Salvatore La Cavera
- Optics & Photonics Group, Faculty of Engineering, University of Nottingham, United Kingdom
| | - Timm Landes
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Germany
| | - Jinhao Li
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Germany
| | - Jeremie Margueritat
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, France
| | | | - Michael Monaghan
- Discipline of Mechanical, Manufacturing & Biomedical Engineering, Trinity College Dublin, Ireland
| | - Darryl R Overby
- Department of Bioengineering, Imperial College London, United Kingdom
| | - Fernando Perez-Cota
- Optics & Photonics Group, Faculty of Engineering, University of Nottingham, United Kingdom
| | | | - Robert Prevedel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Germany
- German Center for Lung Research (DZL), Heidelberg, Germany
| | - Giancarlo Ruocco
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | | | | | | | - Claudia Testi
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Peter Török
- School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore
- Lee Kong Chian School of Medicine, Singapore Centre of Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
- Institute for Digital Molecular Analytics & Sciences, Nanyang Technological University, Singapore
| | - Lucie Vovard
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, France
| | - Wolfgang Weninger
- Center for Anatomy and Cell Biology, Medical University of Vienna, Austria
| | - Vladislav Yakovlev
- Department of Biomedical Engineering, Texas A&M University, USA
- Department of Electrical and Computer Engineering, Texas A&M University, USA
- Department of Physics and Astronomy, Texas A&M University, USA
| | - Seok-Hyun Yun
- Harvard Medical School and Massachusetts General Hospital, USA
| | - Jitao Zhang
- Department of Biomedical Engineering, Wayne State University, USA
| | - Francesca Palombo
- Department of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
| | - Alberto Bilenca
- Biomedical Engineering Department, Ben-Gurion University of the Negev, Israel
| | - Kareem Elsayad
- Center for Anatomy and Cell Biology, Medical University of Vienna, Austria
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19
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Yokoi Y, Nakamura R, Ohira S, Takemi S, Ayabe T, Nakamura K. Potential consequences of phototoxicity on cell function during live imaging of intestinal organoids. PLoS One 2024; 19:e0313213. [PMID: 39546479 PMCID: PMC11567556 DOI: 10.1371/journal.pone.0313213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 10/21/2024] [Indexed: 11/17/2024] Open
Abstract
Live imaging visualizes the structure, dynamics, and function of cells and tissues to reveal the molecular mechanisms, and has contributed to the advancement of life science. In live imaging, it has been well known that there is a trade-off between higher-resolution analysis and cell damage caused by light illumination, i.e., phototoxicity. However, despite the risk of unknowingly distorting experimental results, phototoxicity is an unresolved issue in live imaging because overall consequences occurring inside cells due to phototoxicity remains unknown. Here, we determined the molecular process of phototoxicity-induced cell damage systematically under low- and high-dose light illumination conditions by analyzing differential gene expression using RNA-sequencing in a three-dimensional organoid of small intestinal epithelial cells, enteroid. The low-dose light illumination already induced various abnormalities in functional molecules involved in the response to reactive oxygen species generated by the excitation of fluorescent dyes, intracellular metabolism, mitosis, immune responses, etc., at mRNA expression level. Together with the behavior toward apoptosis caused by high-dose light illumination, the light dose-dependent progression of intracellular damage was revealed. About visible impairment of intestinal epithelial function, failures in both the structure-forming ability of enteroids and Paneth cell granule secretion were observed under high-dose light illumination, while the drug efflux was not disturbed despite abnormal drug efflux transporter mRNA expression. Based on the gene expression profiles, we comprehensively clarified phenomena in the cells at mRNA level that cannot be recognized both morphologically and functionally during live imaging, further providing a new insight into the risk of phototoxicity. This study warns from the aspect of mRNA expression that awareness of phototoxic artifacts is needed when analyzing cellular function and the mechanism in live imaging.
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Affiliation(s)
- Yuki Yokoi
- Innate Immunity Laboratory, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ryu Nakamura
- System Development Section, Technology Solution Sector, Healthcare Business Unit, Nikon Corporation, Yokohama-City, Kanagawa, Japan
| | - Shuya Ohira
- Innate Immunity Laboratory, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Creative Research Institution, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shota Takemi
- Innate Immunity Laboratory, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Tokiyoshi Ayabe
- Innate Immunity Laboratory, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kiminori Nakamura
- Innate Immunity Laboratory, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
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20
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Thomas N, Lyu M, Khouv J, Lima D, Kuss S. Effects of media composition and light exposure on the electrochemical current response during scanning electrochemical microscopy live cell imaging. Analyst 2024; 149:5555-5562. [PMID: 39449279 DOI: 10.1039/d4an01075b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2024]
Abstract
Scanning Electrochemical Microscopy (SECM) has been used as a non-invasive electrochemical technique for studying cellular processes. SECM enables the quantification of cellular metabolites in real-time providing a deeper understanding of cellular responses to external stimuli. SECM imaging of living cells requires maintaining an ideal physiological environment to ensure reliable data collection on cellular reactivity. The cellular response can be directly influenced by physicochemical parameters including cell media composition, temperature and light exposure. This research demonstrates the effect of media composition on the electrochemical current signal of adenocarcinoma cervical cancer (HeLa) cells during SECM measurements using ferrocenemethanol as a redox mediator. Investigated media that are commonly used as electrolyte, are phosphate buffered saline (PBS), and Dulbecco's modified Eagle's medium (DMEM) in the absence and presence of fetal bovine serum (FBS). In addition, this research demonstrates that fluctuating light illumination impacts the stability of the cellular electrochemical current response. Our findings reveal that media composition and illumination are important parameters that must be carefully considered and monitored during SECM live cell imaging.
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Affiliation(s)
- Nikita Thomas
- University of Manitoba, Department of Chemistry, Winnipeg, MB, Canada R3T 2N2.
| | - Mengzhen Lyu
- University of Manitoba, Department of Chemistry, Winnipeg, MB, Canada R3T 2N2.
| | - Jadon Khouv
- University of Manitoba, Department of Chemistry, Winnipeg, MB, Canada R3T 2N2.
| | - Dhésmon Lima
- Mount Saint Vincent University, Department of Chemistry and Physics, Halifax, NS, Canada B3M 2J6
| | - Sabine Kuss
- University of Manitoba, Department of Chemistry, Winnipeg, MB, Canada R3T 2N2.
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21
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Kalyviotis K, Pantazis P. Primed conversion: The emerging player of precise and nontoxic photoconversion. J Microsc 2024; 296:154-161. [PMID: 37937409 DOI: 10.1111/jmi.13244] [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: 06/30/2023] [Revised: 10/17/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
In 2015, we reported primed conversion, a novel way to convert green-to-red photoconvertible fluorescent proteins, which emerges as a powerful tool for precision optical imaging. Primed conversion uses the intercept of blue and red-to-far-red light instead of traditional violet or near-UV light illumination which offers a series of advantages. Here, we review the fundamental principles and applications of primed conversion with a focus on its use in single-cell labelling and lineage tracing. We provide a historical perspective of lineage tracing techniques, thereby covering basic principles of fluorescence, photoconvertible fluorescent proteins, and eventually primed conversion. We then present the molecular requirements for primed conversion to take place and showcase how it can be used for dual-colour high-fidelity lineage tracing. Further, we discuss potential future developments of the primed conversion imaging toolkit that can benefit the study of both development and disease progression.
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22
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Liu T, Kompa J, Ling J, Lardon N, Zhang Y, Chen J, Reymond L, Chen P, Tran M, Yang Z, Zhang H, Liu Y, Pitsch S, Zou P, Wang L, Johnsson K, Chen Z. Gentle Rhodamines for Live-Cell Fluorescence Microscopy. ACS CENTRAL SCIENCE 2024; 10:1933-1944. [PMID: 39463828 PMCID: PMC11503488 DOI: 10.1021/acscentsci.4c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/30/2024] [Accepted: 09/20/2024] [Indexed: 10/29/2024]
Abstract
Rhodamines have been continuously optimized in brightness, biocompatibility, and color to fulfill the demands of modern bioimaging. However, the problem of phototoxicity caused by the excited fluorophore under long-term illumination has been largely neglected, hampering their use in time-lapse imaging. Here we introduce cyclooctatetraene (COT) conjugated rhodamines that span the visible spectrum and exhibit significantly reduced phototoxicity. We identified a general strategy for the generation of Gentle Rhodamines, which preserved their outstanding spectroscopic properties and cell permeability while showing an efficient reduction of singlet-oxygen formation and diminished cellular photodamage. Paradoxically, their photobleaching kinetics do not go hand in hand with reduced phototoxicity. By combining COT-conjugated spirocyclization motifs with targeting moieties, these Gentle Rhodamines compose a toolkit for time-lapse imaging of mitochondria, DNA, and actin, and synergize with covalent and exchangeable HaloTag labeling of cellular proteins with less photodamage than their commonly used precursors. Taken together, the Gentle Rhodamines generally offer alleviated phototoxicity and allow advanced video recording applications, including voltage imaging.
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Affiliation(s)
- Tianyan Liu
- 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, Academy for Advanced Interdisciplinary Studies,
State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Julian Kompa
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Heidelberg 69120, Germany
| | - Jing Ling
- 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, Academy for Advanced Interdisciplinary Studies,
State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Nicolas Lardon
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Heidelberg 69120, Germany
| | - Yuan 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
| | - Jingting 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
| | - Luc Reymond
- Biomolecular
Screening Facility, École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Peng Chen
- PKU-Nanjing
Institute of Translational Medicine, Nanjing 211800, China
- GenVivo
Tech, Nanjing 211800, China
| | - Mai Tran
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Heidelberg 69120, Germany
| | - Zhongtian Yang
- 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, Academy for Advanced Interdisciplinary Studies,
State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Haolin 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
- Peking-Tsinghua
Center for Life Science, Academy for Advanced Interdisciplinary Studies,
State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Yitong Liu
- 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, Academy for Advanced Interdisciplinary Studies,
State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Stefan Pitsch
- Spirochrome
AG, Chalberwiedstrasse
4, CH-8260 Stein
am Rhein, Switzerland
| | - Peng Zou
- Peking-Tsinghua
Center for Life Science, Academy for Advanced Interdisciplinary Studies,
State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
- College
of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules
Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory
of Bioorganic Chemistry and Molecular Engineering of the Ministry
of Education, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Lu Wang
- Key
Laboratory of Smart Drug Delivery, Ministry of Education, School of
Pharmacy, Fudan University, 201203 Shanghai, China
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Heidelberg 69120, Germany
- Biomolecular
Screening Facility, École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - 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, Academy for Advanced Interdisciplinary Studies,
State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
- PKU-Nanjing
Institute of Translational Medicine, Nanjing 211800, China
- GenVivo
Tech, Nanjing 211800, China
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23
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Pruccoli A, Zumbusch A. High Sensitivity Stimulated Raman Scattering Microscopy with Electronic Resonance Enhancement. Chemphyschem 2024; 25:e202400309. [PMID: 38923336 DOI: 10.1002/cphc.202400309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
Raman microscopy is an important tool for labelfree microscopy. However, spontaneous Raman microscopy suffers from slow image acquisition rates and susceptibility to fluorescence background. Coherent Raman microsocopy techniques such as coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) microscopy, by contrast, offer fast imaging capability and robustness against sample fluorescence. Yet, their rather low sensitivity impedes their broader application. This review discusses sensitivity enhancement of SRS microscopy to μ ${\mu }$ M detection levels by using electronically pre-resonant excitation. We present the foundations of this approach, discuss its technological implementation, and show first successful applications. A special emphasis is given to outlining new experimental developments allowing novel types of investigations.
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Affiliation(s)
- Andrea Pruccoli
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
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24
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Valbuena FM, Krahn AH, Tokamov SA, Greene AC, Fehon RG, Glick BS. Yellow and oxidation-resistant derivatives of a monomeric superfolder GFP. Mol Biol Cell 2024; 35:mr8. [PMID: 39141403 PMCID: PMC11481703 DOI: 10.1091/mbc.e24-01-0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Fluorescent proteins (FPs) are essential tools in biology. The utility of FPs depends on their brightness, photostability, efficient folding, monomeric state, and compatibility with different cellular environments. Despite the proliferation of available FPs, derivatives of the originally identified Aequorea victoria green fluorescent protein often show superior behavior as fusion tags. We recently generated msGFP2, an optimized monomeric superfolder variant of A. victoria GFP. Here, we describe two derivatives of msGFP2. The monomeric variant msYFP2 is a yellow superfolder FP with high photostability. The monomeric variant moxGFP2 lacks cysteines but retains significant folding stability, so it works well in the lumen of the secretory pathway. These new FPs are useful for common imaging applications.
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Affiliation(s)
- Fernando M. Valbuena
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Adam H. Krahn
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Sherzod A. Tokamov
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Annie C. Greene
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Richard G. Fehon
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Benjamin S. Glick
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
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25
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Rosvold JR, Murray JB, Zanini G, Redding B, Scarcelli G. Impact of polarization pulling on optimal spectrometer design for stimulated Brillouin scattering microscopy. APL PHOTONICS 2024; 9:100807. [PMID: 39463487 PMCID: PMC11503528 DOI: 10.1063/5.0225074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 09/23/2024] [Indexed: 10/29/2024]
Abstract
Brillouin spectroscopy has become an important tool for mapping the mechanical properties of biological samples. Recently, stimulated Brillouin scattering (SBS) measurements have emerged in this field as a promising technology for lower noise and higher speed measurements. However, further improvements are fundamentally limited by constraints on the optical power level that can be used in biological samples, which effectively caps the gain and signal-to-noise ratio (SNR) of SBS biological measurements. This limitation is compounded by practical limits on the optical probe power due to detector saturation thresholds. As a result, SBS-based measurements in biological samples have provided minimal improvements (in noise and imaging speed) compared with spontaneous Brillouin microscopy, despite the potential advantages of the nonlinear scattering process. Here, we consider how a SBS spectrometer can circumvent this fundamental trade-off in the low-gain regime by leveraging the polarization dependence of the SBS interaction to effectively filter the signal from the background light via the polarization pulling effect. We present an analytic model of the polarization pulling detection scheme and describe the trade-space unique to Brillouin microscopy applications. We show that an optimized receiver design could provide >25× improvement in SNR compared to a standard SBS receiver in most typical experimental conditions. We then experimentally validate this model using optical fiber as a simplified test bed. With our experimental parameters, we find that the polarization pulling scheme provides 100× higher SNR than a standard SBS receiver, enabling 100× faster measurements in the low-gain regime. Finally, we discuss the potential for this proposed spectrometer design to benefit low-gain spectroscopy applications such as Brillouin microscopy by enabling pixel dwell times as short as 10 μs.
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Affiliation(s)
- Jake R. Rosvold
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, College Park, Maryland 20742, USA
| | - Joseph B. Murray
- U.S. Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, District of Columbia 20375, USA
| | - Giulia Zanini
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, College Park, Maryland 20742, USA
| | - Brandon Redding
- U.S. Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, District of Columbia 20375, USA
| | - Giuliano Scarcelli
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, College Park, Maryland 20742, USA
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26
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Ranjan AD, Bhowmick S, Gupta A, Mallick AI, Banerjee A. Biologically Active Micropatterns of Biomolecules and Living Matter Using Microbubble Lithography. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2401127. [PMID: 38884187 DOI: 10.1002/smll.202401127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/17/2024] [Indexed: 06/18/2024]
Abstract
In situ patterning of biomolecules and living organisms while retaining their biological activity is extremely challenging, primarily because such patterning typically involves thermal stresses that could be substantially higher than the physiological thermal or stress tolerance level. Top-down patterning approaches are especially prone to these issues, while bottom-up approaches suffer from a lack of control in developing defined structures and the time required for patterning. A microbubble generated and manipulated by optical tweezers (microbubble lithography) is used to self-assemble and pattern living organisms in continuous microscopic structures in real-time, where the material thus patterned remains biologically active due to their ability to withstand elevated temperatures for short exposures. Successful patterns of microorganisms (Escherichia coli, Lactococcus. lactis and the Type A influenza virus) are demonstrated, as well as reporter proteins such as green fluorescent protein (GFP) on functionalized substrates with high signal-to-noise ratio and selectivity. Together, the data presented herein may open up fascinating possibilities in rapid in situ parallelized diagnostics of multiple pathogens and bioelectronics.
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Affiliation(s)
- Anand Dev Ranjan
- Department of Physical Sciences, IISER Kolkata, Mohanpur, West Bengal, 741246, India
| | - Sucharita Bhowmick
- Department of Biological Sciences, IISER Kolkata, Mohanpur, West Bengal, 741246, India
| | - Arnab Gupta
- Department of Biological Sciences, IISER Kolkata, Mohanpur, West Bengal, 741246, India
| | - Amirul Islam Mallick
- Department of Biological Sciences, IISER Kolkata, Mohanpur, West Bengal, 741246, India
| | - Ayan Banerjee
- Department of Physical Sciences, IISER Kolkata, Mohanpur, West Bengal, 741246, India
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27
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Zhao Q, Wang R, Zhang S, Wang T, Song P, Zheng G. Deep-ultraviolet Fourier ptychography (DUV-FP) for label-free biochemical imaging via feature-domain optimization. APL PHOTONICS 2024; 9:090801. [PMID: 39301193 PMCID: PMC11409226 DOI: 10.1063/5.0227038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024]
Abstract
We present deep-ultraviolet Fourier ptychography (DUV-FP) for high-resolution chemical imaging of biological specimens in their native state without exogenous stains. This approach uses a customized 265-nm DUV LED array for angle-varied illumination, leveraging the unique DUV absorption properties of biomolecules at this wavelength region. We implemented a robust feature-domain optimization framework to overcome common challenges in Fourier ptychographic reconstruction, including vignetting, pupil aberrations, stray light problems, intensity variations, and other systematic errors. By using a 0.12 numerical aperture low-resolution objective lens, our DUV-FP prototype can resolve the 345-nm linewidth on a resolution target, demonstrating at least a four-fold resolution gain compared to the captured raw images. Testing on various biospecimens demonstrates that DUV-FP significantly enhances absorption-based chemical contrast and reveals detailed structural and molecular information. To further address the limitations of conventional FP in quantitative phase imaging, we developed a spatially coded DUV-FP system. This platform enables true quantitative phase imaging of biospecimens with DUV light, overcoming the non-uniform phase response inherent in traditional microscopy techniques. The demonstrated advancements in high-resolution, label-free chemical imaging may accelerate developments in digital pathology, potentially enabling rapid, on-site analysis of biopsy samples in clinical settings.
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Affiliation(s)
- Qianhao Zhao
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Ruihai Wang
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Shuhe Zhang
- University Eye Clinic Maastricht, Maastricht University Medical Center, Maastricht AZ 6202, The Netherlands
| | - Tianbo Wang
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Pengming Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
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28
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Zheng C, Zhang S, Yang D, Chen Z, Li X, Hao Q. Single-shot intensity diffraction tomography via polarization-multiplexed LED illumination. OPTICS LETTERS 2024; 49:4859-4862. [PMID: 39207982 DOI: 10.1364/ol.533430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
We present a single-shot intensity diffraction tomography method via polarization-multiplexed LED illumination. Three LED elements covered with 0°, 45°, and 135° linear polarizers, respectively, are lit up simultaneously to illuminate the sample with illumination angles matching the numerical aperture of the objective. The scattering field of the sample is recorded on a single intensity image with a polarization sensor, and three intensity images corresponding to the three LED elements are decoupled from the intensity image by using a pre-calibrated intensity transform matrix. After a slice-wise deconvolution procedure, the 3D complex refractive index distribution of the sample can be recovered. To demonstrate the performance of our method, we perform experiments on a USAF absorption resolution target, rat hippocampal cell lines, and spongy spicule. These imaging results show that our method can achieve 3D tomography for various biomedical samples with a near incoherent diffraction-limited lateral resolution of 690 nm and an axial resolution of 4.68 μm.
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29
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Gentner C, Rogez B, Robert HML, Aggoun A, Tessier G, Bon P, Berto P. Enhanced Quantitative Wavefront Imaging for Nano-Object Characterization. ACS NANO 2024; 18:19247-19256. [PMID: 38981602 PMCID: PMC11271181 DOI: 10.1021/acsnano.4c05152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]
Abstract
Quantitative phase imaging enables precise and label-free characterizations of individual nano-objects within a large volume, without a priori knowledge of the sample or imaging system. While emerging common path implementations are simple enough to promise a broad dissemination, their phase sensitivity still falls short of precisely estimating the mass or polarizability of vesicles, viruses, or nanoparticles in single-shot acquisitions. In this paper, we revisit the Zernike filtering concept, originally crafted for intensity-only detectors, with the aim of adapting it to wavefront imaging. We demonstrate, through numerical simulation and experiments based on high-resolution wavefront sensing, that a simple Fourier-plane add-on can significantly enhance phase sensitivity for subdiffraction objects─achieving over an order of magnitude increase (×12)─while allowing the quantitative retrieval of both intensity and phase. This advancement allows for more precise nano-object detection and metrology.
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Affiliation(s)
- Clémence Gentner
- Institut
de la Vision, Sorbonne Université, CNRS-UMR 7210, Inserm-UMR
S968, Paris 75012, France
| | - Benoit Rogez
- Institut
de la Vision, Sorbonne Université, CNRS-UMR 7210, Inserm-UMR
S968, Paris 75012, France
- L2n,
Université de technologie de Troyes, CNRS-UMR 7076, Troyes 10004, France
| | - Hadrien M. L. Robert
- Institut
de la Vision, Sorbonne Université, CNRS-UMR 7210, Inserm-UMR
S968, Paris 75012, France
| | - Anis Aggoun
- Institut
de la Vision, Sorbonne Université, CNRS-UMR 7210, Inserm-UMR
S968, Paris 75012, France
| | - Gilles Tessier
- Institut
de la Vision, Sorbonne Université, CNRS-UMR 7210, Inserm-UMR
S968, Paris 75012, France
| | - Pierre Bon
- Université
de Limoges, CNRS, XLIM, UMR 7252, Limoges 87000, France
| | - Pascal Berto
- Institut
de la Vision, Sorbonne Université, CNRS-UMR 7210, Inserm-UMR
S968, Paris 75012, France
- Université
Paris Cité, Paris 75006, France
- Institut
Universitaire de France (IUF), Paris 75231, France
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30
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Chen S, Wang J, Guan D, Tan B, Zhai T, Yang L, Han Y, Liu Y, Liu Q, Zhang Y. Near-Infrared Spontaneously Blinking Fluorophores for Live Cell Super-Resolution Imaging with Minimized Phototoxicity. Anal Chem 2024; 96:10860-10869. [PMID: 38889184 DOI: 10.1021/acs.analchem.4c02445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Single-molecule localization microscopy (SMLM) requires high-intensity laser irradiation, typically exceeding kW/cm2, to yield a sufficient photon count. However, this intense visible light exposure incurs substantial cellular toxicity, hindering its use in living cells. Here, we developed a class of near-infrared (NIR) spontaneously blinking fluorophores for SMLM. These NIR fluorophores are a combination of rhodamine spirolactams and merocyanine derivatives, where the rhodamine spirolactam component converts between a bright and dark state based on pH-dependent spirocyclization and merocyanine derivatives shift the excitation wavelength into the infrared. Single-molecule characterizations demonstrated their potential for SMLM. At a moderate power density of 3.93 kW/cm2, these probes exhibit duty cycle as low as 0.18% and an emission rate as high as 26,700 photons/s. Phototoxicity assessment under single-molecule imaging conditions reveals that NIR illumination (721 nm) minimizes harm to living cells. Employing these NIR fluorophores, we successfully captured time-lapse super-resolution tracking of mitochondria at a Fourier ring correlation (FRC) resolution of 69.4 nm and reconstructed the ultrastructures of endoplasmic reticulum (ER) in living cells.
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Affiliation(s)
- Song Chen
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Jing Wang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Daoming Guan
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Baojin Tan
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Tianli Zhai
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Lu Yang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Yuheng Han
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Liu
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Qian Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Yunxiang Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
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31
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Bresci A, Kobayashi-Kirschvink KJ, Cerullo G, Vanna R, So PTC, Polli D, Kang JW. Label-free morpho-molecular phenotyping of living cancer cells by combined Raman spectroscopy and phase tomography. Commun Biol 2024; 7:785. [PMID: 38951178 PMCID: PMC11217291 DOI: 10.1038/s42003-024-06496-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/23/2024] [Indexed: 07/03/2024] Open
Abstract
Accurate, rapid and non-invasive cancer cell phenotyping is a pressing concern across the life sciences, as standard immuno-chemical imaging and omics require extended sample manipulation. Here we combine Raman micro-spectroscopy and phase tomography to achieve label-free morpho-molecular profiling of human colon cancer cells, following the adenoma, carcinoma, and metastasis disease progression, in living and unperturbed conditions. We describe how to decode and interpret quantitative chemical and co-registered morphological cell traits from Raman fingerprint spectra and refractive index tomograms. Our multimodal imaging strategy rapidly distinguishes cancer phenotypes, limiting observations to a low number of pristine cells in culture. This synergistic dataset allows us to study independent or correlated information in spectral and tomographic maps, and how it benefits cell type inference. This method is a valuable asset in biomedical research, particularly when biological material is in short supply, and it holds the potential for non-invasive monitoring of cancer progression in living organisms.
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Affiliation(s)
- Arianna Bresci
- G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Physics, Politecnico di Milano, Milan, 20133, Italy.
| | - Koseki J Kobayashi-Kirschvink
- G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Giulio Cerullo
- Department of Physics, Politecnico di Milano, Milan, 20133, Italy
- CNR-Institute for Photonics and Nanotechnologies (CNR-IFN), Milan, 20133, Italy
| | - Renzo Vanna
- CNR-Institute for Photonics and Nanotechnologies (CNR-IFN), Milan, 20133, Italy
| | - Peter T C So
- G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Dario Polli
- Department of Physics, Politecnico di Milano, Milan, 20133, Italy.
- CNR-Institute for Photonics and Nanotechnologies (CNR-IFN), Milan, 20133, Italy.
| | - Jeon Woong Kang
- G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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32
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Li Y, Bai X, Yang D. Development and Application of Cationic Nile Blue Probes in Live-Cell Super-Resolution Imaging and Specific Targeting to Mitochondria. ACS CENTRAL SCIENCE 2024; 10:1221-1230. [PMID: 38947205 PMCID: PMC11212141 DOI: 10.1021/acscentsci.4c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/28/2024] [Accepted: 05/09/2024] [Indexed: 07/02/2024]
Abstract
Mitochondria are essential organelles involved in various metabolic processes in eukaryotes. The imaging, targeting, and investigation of cell death mechanisms related to mitochondria have garnered significant interest. Small-molecule fluorescent probes have proven to be robust tools for utilizing light to advance the study of mitochondrial biology. In this study, we present the rational design of cationic Nile blue probes carrying a permanent positive charge for these purposes. The cationic Nile blue probes exhibit excellent mitochondrial permeability, unique solvatochromism, and resistance to oxidation. We observed weaker fluorescence in aqueous solutions compared to lipophilic solvents, thereby minimizing background fluorescence in the cytoplasm. Additionally, we achieved photoredox switching of the cationic Nile blue probes under mild conditions. This enabled us to demonstrate their application for the first time in single-molecule localization microscopy of mitochondria, allowing us to observe mitochondrial fission and fusion behaviors. Compared to conventional cyanine fluorophores, this class of dyes demonstrated prolonged resistance to photobleaching, likely due to their antioxidation properties. Furthermore, we extended the application of cationic Nile blue probes to the mitochondria-specific delivery of taxanes, facilitating the study of direct interactions between the drug and organelles. Our approach to triggering cell death without reliance on microtubule binding provides valuable insights into anticancer drug research and drug-resistance mechanisms.
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Affiliation(s)
- Yunsheng Li
- School
of Life Sciences, Westlake University, Hangzhou 310024, China
- Morningside
Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Xiaoyu Bai
- Morningside
Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Dan Yang
- School
of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake
Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
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33
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Saladin L, Breton V, Le Berruyer V, Nazac P, Lequeu T, Didier P, Danglot L, Collot M. Targeted Photoconvertible BODIPYs Based on Directed Photooxidation-Induced Conversion for Applications in Photoconversion and Live Super-Resolution Imaging. J Am Chem Soc 2024; 146:17456-17473. [PMID: 38861358 DOI: 10.1021/jacs.4c05231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Photomodulable fluorescent probes are drawing increasing attention due to their applications in advanced bioimaging. Whereas photoconvertible probes can be advantageously used in tracking, photoswitchable probes constitute key tools for single-molecule localization microscopy to perform super-resolution imaging. Herein, we shed light on a red and far-red BODIPY, namely, BDP-576 and BDP-650, which possess both properties of conversion and switching. Our study demonstrates that these pyrrolyl-BODIPYs convert into typical green- and red-emitting BODIPYs that are perfectly adapted to microscopy. We also showed that this pyrrolyl-BODIPYs undergo Directed Photooxidation Induced Conversion, a photoconversion mechanism that we recently introduced, where the pyrrole moiety plays a central role. These unique features were used to develop targeted photoconvertible probes toward different organelles or subcellular units (plasma membrane, mitochondria, nucleus, actin, Golgi apparatus, etc.) using chemical targeting moieties and a Halo tag. We notably showed that BDP-650 could be used to track intracellular vesicles over more than 20 min in two-color imagings with laser scanning confocal microscopy, demonstrating its robustness. The switching properties of these photoconverters were studied at the single-molecule level and were then successfully used in live single-molecule localization microscopy in epithelial cells and neurons. Both membrane- and mitochondria- targeted probes could be used to decipher membrane 3D architecture and mitochondrial dynamics at the nanoscale. This study builds a bridge between the photoconversion and photoswitching properties of probes undergoing directed photooxidation and shows the versatility and efficacy of this mechanism in advanced live imaging.
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Affiliation(s)
- Lazare Saladin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Victor Breton
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane Traffic in Healthy and Diseased Brain team; NeurImag core facility scientific director, 75014 Paris, France
| | - Valentine Le Berruyer
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
- Chemistry of Photoresponsive Systems, Laboratoire de Chémo-Biologie Synthétique et Thérapeutique (CBST) UMR 7199, CNRS, Université de Strasbourg, F-67400 Illkirch, France
| | - Paul Nazac
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane Traffic in Healthy and Diseased Brain team; NeurImag core facility scientific director, 75014 Paris, France
| | - Thiebault Lequeu
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Lydia Danglot
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane Traffic in healthy and Diseased brain team; NeurImag core facility scientific director, 75014 Paris, France
| | - Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
- Chemistry of Photoresponsive Systems, Laboratoire de Chémo-Biologie Synthétique et Thérapeutique (CBST) UMR 7199, CNRS, Université de Strasbourg, F-67400 Illkirch, France
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34
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Chow DJX, Tan TCY, Upadhya A, Lim M, Dholakia K, Dunning KR. Viewing early life without labels: optical approaches for imaging the early embryo†. Biol Reprod 2024; 110:1157-1174. [PMID: 38647415 PMCID: PMC11180623 DOI: 10.1093/biolre/ioae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/26/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024] Open
Abstract
Embryo quality is an important determinant of successful implantation and a resultant live birth. Current clinical approaches for evaluating embryo quality rely on subjective morphology assessments or an invasive biopsy for genetic testing. However, both approaches can be inherently inaccurate and crucially, fail to improve the live birth rate following the transfer of in vitro produced embryos. Optical imaging offers a potential non-invasive and accurate avenue for assessing embryo viability. Recent advances in various label-free optical imaging approaches have garnered increased interest in the field of reproductive biology due to their ability to rapidly capture images at high resolution, delivering both morphological and molecular information. This burgeoning field holds immense potential for further development, with profound implications for clinical translation. Here, our review aims to: (1) describe the principles of various imaging systems, distinguishing between approaches that capture morphological and molecular information, (2) highlight the recent application of these technologies in the field of reproductive biology, and (3) assess their respective merits and limitations concerning the capacity to evaluate embryo quality. Additionally, the review summarizes challenges in the translation of optical imaging systems into routine clinical practice, providing recommendations for their future development. Finally, we identify suitable imaging approaches for interrogating the mechanisms underpinning successful embryo development.
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Affiliation(s)
- Darren J X Chow
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
- Centre of Light for Life, The University of Adelaide, Adelaide, Australia
| | - Tiffany C Y Tan
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
| | - Avinash Upadhya
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
- Centre of Light for Life, The University of Adelaide, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Megan Lim
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
- Centre of Light for Life, The University of Adelaide, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Kishan Dholakia
- Centre of Light for Life, The University of Adelaide, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom
| | - Kylie R Dunning
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
- Centre of Light for Life, The University of Adelaide, Adelaide, Australia
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35
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Tobiasz P, Borys F, Kucharska M, Poterała M, Krawczyk H. Synthesis and Study of Building Blocks with Dibenzo[ b,f]oxepine: Potential Microtubule Inhibitors. Int J Mol Sci 2024; 25:6155. [PMID: 38892342 PMCID: PMC11172465 DOI: 10.3390/ijms25116155] [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: 03/13/2024] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The synthesis of biphenylmethoxydibenzo[b,f]oxepine or photoswitchable fluorinated dibenzo[b,f]oxepine derivatives with one or three azo bonds, potential microtubule inhibitors, is described. Our studies provide a concise method for constructing derivatives containing the dibenzo[b,f]oxepine skeleton. An analysis of products was run using experimental and theoretical methods. Next, we evaluated the E/Z isomerization of azo-dibenzo[b,f]oxepine derivatives, which could be photochemically controlled using visible-wavelength light.
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Affiliation(s)
- Piotr Tobiasz
- Department of Organic Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (F.B.); (M.K.); (M.P.)
| | - Filip Borys
- Department of Organic Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (F.B.); (M.K.); (M.P.)
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Marta Kucharska
- Department of Organic Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (F.B.); (M.K.); (M.P.)
| | - Marcin Poterała
- Department of Organic Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (F.B.); (M.K.); (M.P.)
| | - Hanna Krawczyk
- Department of Organic Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (F.B.); (M.K.); (M.P.)
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36
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Rasaily M, Ngiimei D S, Thaosen RK, Gupta S, Deka S, Tamuli R. Methods for the detection of intracellular calcium in filamentous fungi. MethodsX 2024; 12:102570. [PMID: 38322134 PMCID: PMC10844858 DOI: 10.1016/j.mex.2024.102570] [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: 04/19/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
Calcium (Ca2+), a critical secondary messenger, is also known as the molecule of life and death. The cell responds to a minute change in Ca2+ concentration and tightly maintains Ca2+ homeostasis. Therefore, determining the cell Ca2+ level is critical to understand Ca2+ distribution in the cell and various cell processes. Many techniques have been developed to measure Ca2+ in the cell. We review here different methods used to detect and measure Ca2+ in filamentous fungi. Ca2+-sensitive fluorescent chlortetracycline hydrochloride (CTC), Ca2+-selective microelectrode, Ca2+ isotopes, aequorins, and RGECOs are commonly used to measure the Ca2+ level in filamentous fungi. The use of CTC was one of the earliest methods, developed in 1988, to measure the Ca2+ gradient in the filamentous fungus Neurospora crassa. Subsequently, Ca2+-specific microelectrodes were developed later in the 1990s to identify Ca2+ ion flux variations, and to measure Ca2+ concentration. Another method for quantifying Ca2+ is by using radio-labeled Ca2+ as a tracer. The usage of 45Ca to measure Ca2+ in Saccharomyces cerevisiae was reported previously and the same methodology was also used to detect Ca2+ in N. crassa recently. Subsequently, genetically engineered Ca2+ indicators (GECIs) like aequorins and RGECOs have been developed as Ca2+ indicators to detect and visualize Ca2+ inside the cell. In this review, we summarize various methodologies used to detect and measure Ca2+ in filamentous fungi with their advantages and limitations. •Chlortetracycline (CTC) fluorescence assay is used for visualizing Ca2+ level, whereas microelectrodes technique is used to determine Ca2+ flux in the cell.•Radioactive 45Ca is useful for quantification of Ca2+ in the cellular compartments.•Genetically modified calcium indicators (GECIs) are used to study Ca2+ dynamics in the cell.
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Affiliation(s)
- Megha Rasaily
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Serena Ngiimei D
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Rahul Kumar Thaosen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Surabhi Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Sangeeta Deka
- Centre for the Environment, Indian Institute of Technology Guwahati, India
| | - Ranjan Tamuli
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
- Centre for the Environment, Indian Institute of Technology Guwahati, India
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37
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Chen H, Yan G, Wen MH, Brooks KN, Zhang Y, Huang PS, Chen TY. Advancements and Practical Considerations for Biophysical Research: Navigating the Challenges and Future of Super-resolution Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:331-344. [PMID: 38817319 PMCID: PMC11134610 DOI: 10.1021/cbmi.4c00019] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 06/01/2024]
Abstract
The introduction of super-resolution microscopy (SRM) has significantly advanced our understanding of cellular and molecular dynamics, offering a detailed view previously beyond our reach. Implementing SRM in biophysical research, however, presents numerous challenges. This review addresses the crucial aspects of utilizing SRM effectively, from selecting appropriate fluorophores and preparing samples to analyzing complex data sets. We explore recent technological advancements and methodological improvements that enhance the capabilities of SRM. Emphasizing the integration of SRM with other analytical methods, we aim to overcome inherent limitations and expand the scope of biological insights achievable. By providing a comprehensive guide for choosing the most suitable SRM methods based on specific research objectives, we aim to empower researchers to explore complex biological processes with enhanced precision and clarity, thereby advancing the frontiers of biophysical research.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Guangjie Yan
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Meng-Hsuan Wen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Kameron N. Brooks
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Yuteng Zhang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Pei-San Huang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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38
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Bharadwaj A, Kumar A, Mitra R, Jaganathan BG, Boruah BR. Enhanced fluorescence blinking of AF647 fluorophores in Mowiol via violet and UV light induced recovery for superior localization microscopy. Methods Appl Fluoresc 2024; 12:035007. [PMID: 38740072 DOI: 10.1088/2050-6120/ad4ae6] [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: 12/23/2023] [Accepted: 05/13/2024] [Indexed: 05/16/2024]
Abstract
Blinking of fluorophores is essential in the context of single molecule localization-based optical super-resolution microscopy methods. To make the fluorescence molecule undergo blinking specific complex chemical mounting buffer systems, combined with suitable oxygen scavengers, and reducing agents are required. For instance to realise blinking in widely used fluorescence tags, like Alexa Fluor 647 (AF647), they are to be mounted on anti-fading buffer such as Mowiol and reducing agent such as Beta (β) - ME. However, the quality of the super-resolved images is decided by the total number of blinking events or in other words net duration for which the fluorescence blinking persists. In this paper we investigate how a violet and UV light induced fluorescence recovery mechanism can enhance the duration of fluorescence blinking. Our study uses AF647 dye conjugated with Phalloidin antibody in U87MG cell line mounted on Mowiol andβ- ME. On the basis of the investigation we optimize the intensity, at the sample plane, of fluorescence excitation laser at 638 nm and fluorescence recovery beam at 405 nm or in the UV giving the maximum possible fluorescence blinking duration. We observe that the longer blinking duration, using the optimized illumination scheme, has brought down the resolution in the super-resolved image, as given by Fourier Ring Correlation method, from 168 nm to 112 nm, while the separation between two nearby resolvable filaments has been brought down to ≤ 60 nm.
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Affiliation(s)
- Anupam Bharadwaj
- Department of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Amalesh Kumar
- Department of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Rumela Mitra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Bithiah Grace Jaganathan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Bosanta R Boruah
- Department of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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39
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Kasprzycka W, Szumigraj W, Wachulak P, Trafny EA. New approaches for low phototoxicity imaging of living cells and tissues. Bioessays 2024; 46:e2300122. [PMID: 38514402 DOI: 10.1002/bies.202300122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024]
Abstract
Fluorescence microscopy is a powerful tool used in scientific and medical research, but it is inextricably linked to phototoxicity. Neglecting phototoxicity can lead to erroneous or inconclusive results. Recently, several reports have addressed this issue, but it is still underestimated by many researchers, even though it can lead to cell death. Phototoxicity can be reduced by appropriate microscopic techniques and carefully designed experiments. This review focuses on recent strategies to reduce phototoxicity in microscopic imaging of living cells and tissues. We describe digital image processing and new hardware solutions. We point out new modifications of microscopy methods and hope that this review will interest microscopy hardware engineers. Our aim is to underscore the challenges and potential solutions integral to the design of microscopy systems. Simultaneously, we intend to engage biologists, offering insight into the latest technological advancements in imaging that can enhance their understanding and practice.
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Affiliation(s)
- Wiktoria Kasprzycka
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, Kaliskiego, Warsaw, Poland
| | - Wiktoria Szumigraj
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, Kaliskiego, Warsaw, Poland
| | - Przemysław Wachulak
- Laser Technology Division, Institute of Optoelectronics, Military University of Technology, Kaliskiego, Warsaw, Poland
| | - Elżbieta Anna Trafny
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, Kaliskiego, Warsaw, Poland
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40
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Ahmadian S, Lindsey PJ, Smeets HJM, van Tienen FHJ, van Zandvoort MAMJ. Spinning Disk Confocal Microscopy for Optimized and Quantified Live Imaging of 3D Mitochondrial Network. Int J Mol Sci 2024; 25:4819. [PMID: 38732037 PMCID: PMC11083894 DOI: 10.3390/ijms25094819] [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: 03/24/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Mitochondria are the energy factories of a cell, and depending on the metabolic requirements, the mitochondrial morphology, quantity, and membrane potential in a cell change. These changes are frequently assessed using commercially available probes. In this study, we tested the suitability of three commercially available probes-namely 5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolo-carbocyanine iodide (JC-1), MitoTracker Red CMX Rox (CMXRos), and tetramethylrhodamine methyl ester (TMRM)-for assessing the mitochondrial quantity, morphology, and membrane potential in living human mesoangioblasts in 3D with confocal laser scanning microscope (CLSM) and scanning disk confocal microscope (SDCM). Using CLSM, JC-1, and CMXRos-but not TMRM-uncovered considerable background and variation. Using SDCM, the background signal only remained apparent for the JC-1 monomer. Repetitive imaging of CMXRos and JC-1-but not TMRM-demonstrated a 1.5-2-fold variation in signal intensity between cells using CLSM. The use of SDCM drastically reduced this variation. The slope of the relative signal intensity upon repetitive imaging using CLSM was lowest for TMRM (-0.03) and highest for CMXRos (0.16). Upon repetitive imaging using SDCM, the slope varied from 0 (CMXRos) to a maximum of -0.27 (JC-1 C1). Conclusively, our data show that TMRM staining outperformed JC-1 and CMXRos dyes in a (repetitive) 3D analysis of the entire mitochondrial quantity, morphology, and membrane potential in living cells.
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Affiliation(s)
- Somaieh Ahmadian
- Department of Toxicogenomics, Maastricht University Medical Centre+, 6229 ER Maastricht, The Netherlands; (P.J.L.); (H.J.M.S.); (F.H.J.v.T.)
- GROW Research Institute for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
- Department of Genetics and Molecular Cell Biology, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Patrick J. Lindsey
- Department of Toxicogenomics, Maastricht University Medical Centre+, 6229 ER Maastricht, The Netherlands; (P.J.L.); (H.J.M.S.); (F.H.J.v.T.)
- GROW Research Institute for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Hubert J. M. Smeets
- Department of Toxicogenomics, Maastricht University Medical Centre+, 6229 ER Maastricht, The Netherlands; (P.J.L.); (H.J.M.S.); (F.H.J.v.T.)
- GROW Research Institute for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
- Institutefor Mental Health and Neurosciences (MHeNS), Maastricht University Medical Centre+, 6229 ER Maastricht, The Netherlands
| | - Florence H. J. van Tienen
- Department of Toxicogenomics, Maastricht University Medical Centre+, 6229 ER Maastricht, The Netherlands; (P.J.L.); (H.J.M.S.); (F.H.J.v.T.)
- Institutefor Mental Health and Neurosciences (MHeNS), Maastricht University Medical Centre+, 6229 ER Maastricht, The Netherlands
| | - Marc A. M. J. van Zandvoort
- GROW Research Institute for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
- Department of Genetics and Molecular Cell Biology, Maastricht University, 6229 ER Maastricht, The Netherlands
- Institutefor Mental Health and Neurosciences (MHeNS), Maastricht University Medical Centre+, 6229 ER Maastricht, The Netherlands
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
- IMCAR, Institute for Molecular Cardiovascular Research, Universitätsklinikum Aachen, 52074 Aachen, Germany
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41
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Matsuda T, Sakai S, Okazaki KI, Nagai T. Improvement of the Green-Red Förster Resonance Energy Transfer-Based Ca 2+ Indicator by Using the Green Fluorescent Protein, Gamillus, with a Trans Chromophore as the Donor. ACS Sens 2024; 9:1743-1748. [PMID: 38515268 PMCID: PMC11059083 DOI: 10.1021/acssensors.3c02398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
To monitor the Ca2+ dynamics in cells, various genetically encoded Ca2+ indicators (GECIs) based on Förster resonance energy transfer (FRET) between fluorescent proteins are widely used for live imaging. Conventionally, cyan and yellow fluorescent proteins have been often used as FRET pairs. Meanwhile, bathochromically shifted indicators with green and red fluorescent protein pairs have various advantages, such as low toxicity and autofluorescence in cells. However, it remains difficult to develop them with a similar level of dynamic range as cyan and yellow fluorescent protein pairs. To improve this, we used Gamillus, which has a unique trans-configuration chromophore, as a green fluorescent protein. Based on one of the best high-dynamic-range GECIs, Twitch-NR, we developed a GECI with 1.5-times higher dynamic range (253%), Twitch-GmRR, using RRvT as a red fluorescent protein. Twitch-GmRR had high brightness and photostability and was successfully applied for imaging the Ca2+ dynamics in live cells. Our results suggest that Gamillus with trans-type chromophores contributes to improving the dynamic range of GECIs. Therefore, selection of the cis-trans isomer of the chromophore may be a fundamental approach to improve the dynamic range of green-red FRET indicators, unlimited by GECIs.
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Affiliation(s)
- Tomoki Matsuda
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Shinya Sakai
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kei-ichi Okazaki
- Research
Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- Graduate
Institute for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8585, Japan
| | - Takeharu Nagai
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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42
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Dani S, Schütz K, Dikici E, Bernhardt A, Lode A. The effect of continuous long-term illumination with visible light in different spectral ranges on mammalian cells. Sci Rep 2024; 14:9444. [PMID: 38658667 PMCID: PMC11043379 DOI: 10.1038/s41598-024-60014-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
One of the biggest challenges in tissue engineering and regenerative medicine is to ensure oxygen supply of cells in the (temporary) absence of vasculature. With the vision to exploit photosynthetic oxygen production by microalgae, co-cultivated in close vicinity to oxygen-consuming mammalian cells, we are searching for culture conditions that are compatible for both sides. Herein, we investigated the impact of long-term illumination on mammalian cells which is essential to enable photosynthesis by microalgae: four different cell types-primary human fibroblasts, dental pulp stem cells, and osteoblasts as well as the murine beta-cell line INS-1-were continuously exposed to warm white light, red or blue light over seven days. We observed that illumination with red light has no adverse effects on viability, metabolic activity and growth of the cells whereas exposure to white light has deleterious effects that can be attributed to its blue light portion. Quantification of intracellular glutathione did not reveal a clear correlation of this effect with an enhanced production of reactive oxygen species. Finally, our data indicate that the cytotoxic effect of short-wavelength light is predominantly a direct effect of cell illumination; photo-induced changes in the cell culture media play only a minor role.
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Affiliation(s)
- Sophie Dani
- Centre for Translational Bone, Joint and Soft Tissue Research, Faculty of Medicine, Technical University Dresden, Dresden, Germany
| | - Kathleen Schütz
- Centre for Translational Bone, Joint and Soft Tissue Research, Faculty of Medicine, Technical University Dresden, Dresden, Germany
| | - Ezgi Dikici
- Centre for Translational Bone, Joint and Soft Tissue Research, Faculty of Medicine, Technical University Dresden, Dresden, Germany
| | - Anne Bernhardt
- Centre for Translational Bone, Joint and Soft Tissue Research, Faculty of Medicine, Technical University Dresden, Dresden, Germany
| | - Anja Lode
- Centre for Translational Bone, Joint and Soft Tissue Research, Faculty of Medicine, Technical University Dresden, Dresden, Germany.
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43
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Khalef L, Lydia R, Filicia K, Moussa B. Cell viability and cytotoxicity assays: Biochemical elements and cellular compartments. Cell Biochem Funct 2024; 42:e4007. [PMID: 38593323 DOI: 10.1002/cbf.4007] [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: 01/10/2024] [Revised: 03/01/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Cell viability and cytotoxicity assays play a crucial role in drug screening and evaluating the cytotoxic effects of various chemicals. The quantification of cell viability and proliferation serves as the cornerstone for numerous in vitro assays that assess cellular responses to external factors. In the last decade, several studies have developed guidelines for defining and interpreting cell viability and cytotoxicity based on morphological, biochemical, and functional perspectives. As this domain continues to experience ongoing growth, revealing new mechanisms orchestrating diverse cell cytotoxicity pathways, we suggest a revised classification for multiple assays employed in evaluating cell viability and cell death. This classification is rooted in the cellular compartment and/or biochemical element involved, with a specific focus on mechanistic and essential aspects of the process. The assays are founded on diverse cell functions, encompassing metabolic activity, enzyme activity, cell membrane permeability and integrity, adenosine 5'-triphosphate content, cell adherence, reduction equivalents, dye inclusion or exclusion, constitutive protease activity, colony formation, DNA fragmentation and nuclear splitting. These assays present straightforward, reliable, sensitive, reproducible, cost-effective, and high-throughput approaches for appraising the effects of newly formulated chemotherapeutic biomolecules on the cell survival during the drug development process.
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Affiliation(s)
- Lefsih Khalef
- Département de Biochimie et Microbiologie, Laboratoire d'Ecologie, Biotechnologie et Santé, Université Mouloud Mammeri de Tizi ouzou, Tizi Ouzou, Algeria
| | - Radja Lydia
- Département de Biochimie et Microbiologie, Laboratoire d'Ecologie, Biotechnologie et Santé, Université Mouloud Mammeri de Tizi ouzou, Tizi Ouzou, Algeria
| | - Khettar Filicia
- Département de Biochimie et Microbiologie, Laboratoire d'Ecologie, Biotechnologie et Santé, Université Mouloud Mammeri de Tizi ouzou, Tizi Ouzou, Algeria
| | - Berkoud Moussa
- Département de Biochimie et Microbiologie, Laboratoire d'Ecologie, Biotechnologie et Santé, Université Mouloud Mammeri de Tizi ouzou, Tizi Ouzou, Algeria
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Sivun D, Murtezi E, Karimian T, Hurab K, Marefat M, Klimareva E, Naderer C, Buchroithner B, Klar TA, Gvindzhiliia G, Horner A, Jacak J. Multiphoton lithography with protein photoresists. Mater Today Bio 2024; 25:100994. [PMID: 38384793 PMCID: PMC10879783 DOI: 10.1016/j.mtbio.2024.100994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/03/2024] [Accepted: 02/04/2024] [Indexed: 02/23/2024] Open
Abstract
Recently, 2D/3D direct laser writing has attracted increased attention due to its broad applications ranging from biomedical engineering to aerospace. 3D nanolithography of water-soluble protein-based scaffolds have been envisioned to provide a variety of tunable properties. In this paper, we present a functional protein-based photoresist with tunable mechanical properties that is suitable for multiphoton lithography (MPL). Through the use of methacrylated streptavidin or methacrylated bovine serum albumin in combination with polyethylene glycol diacrylate or methacrylated hyaluronic acid as crosslinkers and a vitamin-based photoinitiator, we were able to write two- and three-dimensional structures as small as 200 nm/600 nm lateral/axial features, respectively. We also demonstrated that Young's modulus can be tuned by the photoresist composition, and we were able to achieve values as low as 40 kPa. Furthermore, we showed that Young's modulus can be recovered after drying and rehydration (i.e. shelf time determination). The retained biological functionality of the streptavidin scaffolds was demonstrated using fluorescently labelled biotins. Using single-molecule fluorescence microscopy, we estimated the density of streptavidin in the written features (1.8 ± 0.2 × 105 streptavidins per 1.00 ± 0.05 μm³ of feature volume). Finally, we showed applicability of our 2D scaffold as a support for a fluorescence absorbance immuno-assay (FLISA), and as a delivery platform of extracellular vesicles to HeLa cells.
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Affiliation(s)
- Dmitry Sivun
- Department of Medical Engineering, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020, Linz, Austria
| | - Eljesa Murtezi
- Department of Medical Engineering, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020, Linz, Austria
| | - Tina Karimian
- Department of Medical Engineering, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020, Linz, Austria
| | - Kurt Hurab
- Department of Medical Engineering, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020, Linz, Austria
| | - Maryam Marefat
- Department of Medical Engineering, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020, Linz, Austria
| | - Elena Klimareva
- Department of Medical Engineering, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020, Linz, Austria
| | - Christoph Naderer
- Department of Medical Engineering, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020, Linz, Austria
| | - Boris Buchroithner
- Department of Medical Engineering, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020, Linz, Austria
| | - Thomas A. Klar
- Institute of Applied Physics, Johannes Kepler University Linz, Altenberger Straße 69, 4040, Linz, Austria
| | - Georgii Gvindzhiliia
- Institute of Applied Physics, Johannes Kepler University Linz, Altenberger Straße 69, 4040, Linz, Austria
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstraße 40, 4020, Linz, Austria
| | - Jaroslaw Jacak
- Department of Medical Engineering, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020, Linz, Austria
- AUVA Research Center, Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Donaueschingenstraße 13, 1200 Vienna, Austria
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Lee CH, Wallace DC, Burke PJ. Photobleaching and phototoxicity of mitochondria in live cell fluorescent super-resolution microscopy. MITOCHONDRIAL COMMUNICATIONS 2024; 2:38-47. [PMID: 39449993 PMCID: PMC11500826 DOI: 10.1016/j.mitoco.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2024]
Abstract
Photobleaching and phototoxicity can induce detrimental effects on cell viability and compromise the integrity of collected data, particularly in studies utilizing super-resolution microscopes. Given the involvement of multiple factors, it is currently challenging to propose a single set of standards for assessing the potential of phototoxicity. The objective of this paper is to present empirical data on the effects of photobleaching and phototoxicity on mitochondria during super-resolution imaging of mitochondrial structure and function using Airyscan and the fluorescent structure dyes Mitotracker green (MTG), 10-N-nonyl acridine orange (NAO), and voltage dye Tetramethylrhodamine, Ethyl Ester (TMRE). We discern two related phenomena. First, phototoxicity causes a transformation of mitochondria from tubular to spherical shape, accompanied by a reduction in the number of cristae. Second, phototoxicity impacts the mitochondrial membrane potential. Through these parameters, we discovered that upon illumination, NAO is much more phototoxic to mitochondria compared to MTG or TMRE and that these parameters can be used to evaluate the relative phototoxicity of various mitochondrial dye-illumination combinations during mitochondrial imaging.
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Affiliation(s)
- Chia-Hung Lee
- Department of Biomedical Engineering, University of California, Irvine, CA, 92697, United States
| | - Douglas C. Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia and Department of Pediatrics, Division of Human Genetics, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Peter J. Burke
- Department of Electrical Engineering and Computer Science, United States
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Kavčič A, Podlipec R, Krišelj A, Jelen A, Vella D, Humar M. Intracellular biocompatible hexagonal boron nitride quantum emitters as single-photon sources and barcodes. NANOSCALE 2024; 16:4691-4702. [PMID: 38319598 PMCID: PMC10903403 DOI: 10.1039/d3nr05305a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Color centers in hexagonal boron nitride (hBN) have been emerging as a multifunctional platform for various optical applications including quantum information processing, quantum computing and imaging. Simultaneously, due to its biocompatibility and biodegradability hBN is a promising material for biomedical applications. In this work, we demonstrate single-photon emission from hBN color centers embedded inside live cells and their application to cellular barcoding. The generation and internalization of multiple color centers into cells was performed via simple and scalable procedure while keeping the cells unharmed. The emission from live cells was observed as multiple diffraction-limited spots, which exhibited excellent single-photon characteristics with high single-photon purity of 0.1 and superb emission stability without photobleaching or spectral shifts over several hours. Due to different emission wavelengths and peak widths of the color centers, they were employed as barcodes. We term them Quantum Photonic Barcodes (QPBs). Each QPB can exist in one out of 470 possible distinguishable states and a combination of a few QPBs per cell can be used to uniquely tag virtually an unlimited number of cells. The barcodes developed here offer some excellent properties, including ease of production by a single-step procedure, biocompatibility and biodegradability, emission stability, no photobleaching, small size and a huge number of unique barcodes. This work provides a basis for the use of hBN color centers for robust barcoding of cells and due to the single photon emission, presented concepts could in future be extended to quantum-limited sensing and super-resolution imaging.
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Affiliation(s)
- Aljaž Kavčič
- Condensed Matter Department, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia
| | - Rok Podlipec
- Condensed Matter Department, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
- Helmholtz-Zentrum Dresden-Rossendorf e.V., Ion Beam Center, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Ana Krišelj
- Condensed Matter Department, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | - Andreja Jelen
- Condensed Matter Department, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | - Daniele Vella
- Faculty of Mechanical Engineering, Laboratory for Laser Techniques, University of Ljubljana, Aškerčeva 6, SI-1000 Ljubljana, Slovenia
| | - Matjaž Humar
- Condensed Matter Department, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia
- CENN Nanocenter, Jamova 39, SI-1000 Ljubljana, Slovenia
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47
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Gómez-de-Mariscal E, Del Rosario M, Pylvänäinen JW, Jacquemet G, Henriques R. Harnessing artificial intelligence to reduce phototoxicity in live imaging. J Cell Sci 2024; 137:jcs261545. [PMID: 38324353 PMCID: PMC10912813 DOI: 10.1242/jcs.261545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024] Open
Abstract
Fluorescence microscopy is essential for studying living cells, tissues and organisms. However, the fluorescent light that switches on fluorescent molecules also harms the samples, jeopardizing the validity of results - particularly in techniques such as super-resolution microscopy, which demands extended illumination. Artificial intelligence (AI)-enabled software capable of denoising, image restoration, temporal interpolation or cross-modal style transfer has great potential to rescue live imaging data and limit photodamage. Yet we believe the focus should be on maintaining light-induced damage at levels that preserve natural cell behaviour. In this Opinion piece, we argue that a shift in role for AIs is needed - AI should be used to extract rich insights from gentle imaging rather than recover compromised data from harsh illumination. Although AI can enhance imaging, our ultimate goal should be to uncover biological truths, not just retrieve data. It is essential to prioritize minimizing photodamage over merely pushing technical limits. Our approach is aimed towards gentle acquisition and observation of undisturbed living systems, aligning with the essence of live-cell fluorescence microscopy.
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Affiliation(s)
| | | | - Joanna W. Pylvänäinen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku 20500, Finland
| | - Guillaume Jacquemet
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku 20500, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, Åbo Akademi University, Turku 20100, Finland
| | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
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48
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Valbuena FM, Krahn AH, Tokamov SA, Greene AC, Fehon RG, Glick BS. Yellow and oxidation-resistant derivatives of a monomeric superfolder GFP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577236. [PMID: 38328041 PMCID: PMC10849726 DOI: 10.1101/2024.01.25.577236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Fluorescent proteins (FPs) are essential tools in biology. The utility of FPs depends on their brightness, photostability, efficient folding, monomeric state, and compatibility with different cellular environments. Despite the proliferation of available FPs, derivatives of the originally identified Aequorea victoria GFP often show superior behavior as fusion tags. We recently generated msGFP2, an optimized monomeric superfolder variant of A. victoria GFP. Here, we describe two derivatives of msGFP2. The monomeric variant msYFP2 is a yellow superfolder FP with high photostability. The monomeric variant moxGFP2 lacks cysteines but retains significant folding stability, so it works well in the lumen of the secretory pathway. These new FPs are useful for common imaging applications.
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49
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Pain C, Kriechbaumer V, Candeo A. Observing ER Dynamics over Long Timescales Using Light Sheet Fluorescence Microscopy. Methods Mol Biol 2024; 2772:323-335. [PMID: 38411826 DOI: 10.1007/978-1-0716-3710-4_25] [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: 02/28/2024]
Abstract
The recent significant progress in developmental bio-imaging of live multicellular organisms has been greatly facilitated by the development of light sheet fluorescence microscopy (LSFM). Both commercial and custom LSFM systems offer the best means for long-term rapid data collection over a wide field of view at single-cell resolution. This is thanks to the low light exposure required for imaging and consequent limited photodamage to the biological sample, and the development of custom holders and mounting techniques that allow for specimens to be imaged in near-normal physiological conditions. This method has been successfully applied to plant cell biology and is currently seen as one of the most efficient techniques for 3D time-lapse imaging for quantitative studies. LSFM allows one to capture and quantify dynamic processes across various levels, from plant subcellular compartments to whole cells, tissues, and entire plant organs. Here we present a method to carry out LSFM on Arabidopsis leaves expressing fluorescent markers targeted to the ER. We will focus on a protocol to mount the sample, test the phototoxicity of the LSFM system, set up a LSFM experiment, and monitor the dynamics of the ER during heat shock.
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Affiliation(s)
- Charlotte Pain
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Alessia Candeo
- Dipartimento di Fisica, Politecnico di Milano, Milan, Italy.
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, Oxford, UK.
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50
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Shen YJ, Liao EY, Tai TM, Liao YH, Sun CK, Lee CK, See S, Chen HW. Deep learning-based photodamage reduction on harmonic generation microscope at low-level optical power. JOURNAL OF BIOPHOTONICS 2024; 17:e202300285. [PMID: 37738103 DOI: 10.1002/jbio.202300285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
The trade-off between high-quality images and cellular health in optical bioimaging is a crucial problem. We demonstrated a deep-learning-based power-enhancement (PE) model in a harmonic generation microscope (HGM), including second harmonic generation (SHG) and third harmonic generation (THG). Our model can predict high-power HGM images from low-power images, greatly reducing the risk of phototoxicity and photodamage. Furthermore, the PE model trained only on normal skin data can also be used to predict abnormal skin data, enabling the dermatopathologist to successfully identify and label cancer cells. The PE model shows potential for in-vivo and ex-vivo HGM imaging.
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Affiliation(s)
- Yi-Jiun Shen
- International Intercollegiate Ph.D. Program, National Tsing Hua University, Hsinchu, Taiwan
| | - En-Yu Liao
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei, Taiwan
| | | | - Yi-Hua Liao
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chi-Kuang Sun
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei, Taiwan
| | | | - Simon See
- NVIDIA AI Technology Center, NVIDIA, Taipei, Taiwan
| | - Hung-Wen Chen
- International Intercollegiate Ph.D. Program, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan
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