1
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Martinez KN, Gerstner NC, Yang SJ, Miller EW. Extended voltage imaging in cardiomyocytes with a triplet state quencher-stabilized silicon rhodamine. Bioorg Med Chem Lett 2024; 109:129842. [PMID: 38844174 DOI: 10.1016/j.bmcl.2024.129842] [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: 09/29/2023] [Revised: 05/17/2024] [Accepted: 06/02/2024] [Indexed: 06/18/2024]
Abstract
Voltage imaging of cardiac electrophysiology with voltage-sensitive dyes has long been a powerful complement to traditional methods like patch-clamp electrophysiology. Chemically synthesized voltage sensitive fluorophores offer flexibility for imaging in sensitive samples like human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs), since they do not require genetic transformation of the sample. One serious concern for any fluorescent voltage indicator, whether chemically synthesized or genetically encoded, is phototoxicity. We have been exploring self-healing fluorophores that use triplet state quenchers (TSQs) as a means to reduce the already low phototoxicity of VoltageFluor dyes developed in our lab. We previously showed that conjugation of the TSQ cyclooctatetraene (COT) to a fluorescein based VoltageFluor dye substantially reduced phototoxicity. Here, we show that this approach can be applied to far-red Silicon rhodamine dyes. COT-conjugated Si-rhodamines show improved photostability and reduced phototoxicity in hiPSC-CMs compared to the unmodified dye. This enables imaging of hiPSC-CMs for up to 30 min with continuous illumination. We show that this effect is mediated by a combination of reduced singlet oxygen production and lower loading in the cellular membrane. We discuss future applications and avenues of improvement for TSQ-stabilized VoltageFluor dyes.
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Affiliation(s)
- Kayli N Martinez
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720-1460, USA
| | - Nels C Gerstner
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720-1460, USA
| | - Samantha J Yang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720-1460, USA
| | - Evan W Miller
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720-1460, USA; Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720-1460, USA.
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2
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Xia F, Rimoli CV, Akemann W, Ventalon C, Bourdieu L, Gigan S, de Aguiar HB. Neurophotonics beyond the surface: unmasking the brain's complexity exploiting optical scattering. NEUROPHOTONICS 2024; 11:S11510. [PMID: 38617592 PMCID: PMC11014413 DOI: 10.1117/1.nph.11.s1.s11510] [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: 11/08/2023] [Revised: 03/07/2024] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
The intricate nature of the brain necessitates the application of advanced probing techniques to comprehensively study and understand its working mechanisms. Neurophotonics offers minimally invasive methods to probe the brain using optics at cellular and even molecular levels. However, multiple challenges persist, especially concerning imaging depth, field of view, speed, and biocompatibility. A major hindrance to solving these challenges in optics is the scattering nature of the brain. This perspective highlights the potential of complex media optics, a specialized area of study focused on light propagation in materials with intricate heterogeneous optical properties, in advancing and improving neuronal readouts for structural imaging and optical recordings of neuronal activity. Key strategies include wavefront shaping techniques and computational imaging and sensing techniques that exploit scattering properties for enhanced performance. We discuss the potential merger of the two fields as well as potential challenges and perspectives toward longer term in vivo applications.
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Affiliation(s)
- Fei Xia
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
| | - Caio Vaz Rimoli
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Walther Akemann
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Cathie Ventalon
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Laurent Bourdieu
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Sylvain Gigan
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
| | - Hilton B. de Aguiar
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
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3
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Philippi CI, Hagens J, Heuer KM, Schmidt HC, Schuppert P, Pagerols Raluy L, Trochimiuk M, Li Z, Bunders MJ, Reinshagen K, Tomuschat C. Exploring cell death mechanisms in spheroid cultures using a novel application of the RIP3-caspase3-assay. Sci Rep 2024; 14:16032. [PMID: 38992075 DOI: 10.1038/s41598-024-66805-4] [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: 01/15/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024] Open
Abstract
This study explores the application of the RIP3-caspase3-assay in heterogeneous spheroid cultures to analyze cell death pathways, emphasizing the nuanced roles of apoptosis and necroptosis. By employing directly conjugated monoclonal antibodies, we provide detailed insights into the complex mechanisms of cell death. Our findings demonstrate the assay's capability to differentiate between RIP1-independent apoptosis, necroptosis, and RIP1-dependent apoptosis, marking a significant advancement in organoid research. Additionally, we investigate the effects of TNFα on isolated intestinal epithelial cells, revealing a concentration-dependent response and an adaptive or threshold reaction to TNFα-induced stress. The results indicate a preference for RIP1-independent cell death pathways upon TNFα stimulation, with a notable increase in apoptosis and a secondary role of necroptosis. Our research underscores the importance of the RIP3-caspase3-assay in understanding cell death mechanisms in organoid cultures, offering valuable insights for disease modeling and the development of targeted therapies. The assay's adaptability and robustness in spheroid cultures enhances its potential as a tool in personalized medicine and translational research.
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Affiliation(s)
- C I Philippi
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - J Hagens
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - K M Heuer
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - H C Schmidt
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - P Schuppert
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - L Pagerols Raluy
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - M Trochimiuk
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Z Li
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - M J Bunders
- Research Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
- Division of Regenerative Medicine and Immunology, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - K Reinshagen
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - C Tomuschat
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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4
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Landajuela A, Braun M, Rodrigues CDA, Karatekin E. Detection of membrane fission in single Bacillus subtilis cells during endospore formation with high temporal resolution. STAR Protoc 2024; 5:102965. [PMID: 38502684 PMCID: PMC10963649 DOI: 10.1016/j.xpro.2024.102965] [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: 02/23/2023] [Revised: 07/17/2023] [Accepted: 03/01/2024] [Indexed: 03/21/2024] Open
Abstract
Membrane fission is an essential process in all domains of life. The underlying mechanisms remain poorly understood in bacteria, partly because suitable assays are lacking. Here, we describe an assay to detect membrane fission during endospore formation in single Bacillus subtilis cells with a temporal resolution of ∼1 min. Other cellular processes can be quantified and temporally aligned to the membrane fission event in individual cells, revealing correlations and causal relationships. For complete details on the use and execution of this protocol, please refer to Landajuela et al.1.
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Affiliation(s)
- Ane Landajuela
- Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, West Haven, CT, USA.
| | - Martha Braun
- Nanobiology Institute, Yale University, West Haven, CT, USA; Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Erdem Karatekin
- Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, West Haven, CT, USA; Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Université de Paris, Saints-Pères Paris Institute for the Neurosciences (SPPIN), Centre National de la Recherche Scientifique (CNRS), 75006 Paris, France.
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5
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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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6
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Elmalam N, Ben Nedava L, Zaritsky A. In silico labeling in cell biology: Potential and limitations. Curr Opin Cell Biol 2024; 89:102378. [PMID: 38838549 DOI: 10.1016/j.ceb.2024.102378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
In silico labeling is the computational cross-modality image translation where the output modality is a subcellular marker that is not specifically encoded in the input image, for example, in silico localization of organelles from transmitted light images. In principle, in silico labeling has the potential to facilitate rapid live imaging of multiple organelles with reduced photobleaching and phototoxicity, a technology enabling a major leap toward understanding the cell as an integrated complex system. However, five years have passed since feasibility was attained, without any demonstration of using in silico labeling to uncover new biological insight. In here, we discuss the current state of in silico labeling, the limitations preventing it from becoming a practical tool, and how we can overcome these limitations to reach its full potential.
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Affiliation(s)
- Nitsan Elmalam
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Lion Ben Nedava
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Assaf Zaritsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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7
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Badrodien I, Neethling PH, Bosman GW. Improved image contrast in nonlinear light-sheet fluorescence microscopy using i 2 PIE Pulse compression. Sci Rep 2024; 14:12770. [PMID: 38834608 DOI: 10.1038/s41598-024-63429-6] [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: 03/01/2024] [Accepted: 05/29/2024] [Indexed: 06/06/2024] Open
Abstract
Nonlinear microscopy has become an invaluable tool for biological imaging, offering high-resolution visualization of biological specimens. In this manuscript, we present the application of a spectral phase measurement technique, i2 PIE, to compress broad-bandwidth supercontinuum pulses for two-photon excitation fluorescence light-sheet fluorescence microscopy. The results demonstrated a significant improvement in the two-photon excitation response achieved. We also showed that the implementation of i2 PIE allowed for enhanced image contrasts when compared to conventional compression techniques, with i2 PIE producing an image contrast improvement over conventional methods by over 50%.
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Affiliation(s)
- Imraan Badrodien
- Stellenbosch Photonics Institute, Physics Department, Stellenbosch University, Stellenbosch, Western Cape, South Africa
| | - Pieter H Neethling
- Stellenbosch Photonics Institute, Physics Department, Stellenbosch University, Stellenbosch, Western Cape, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Stellenbosch, South Africa
| | - Gurthwin W Bosman
- Stellenbosch Photonics Institute, Physics Department, Stellenbosch University, Stellenbosch, Western Cape, South Africa.
- National Institute for Theoretical and Computational Sciences (NITheCS), Stellenbosch, South Africa.
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8
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Ziegler KF, Joshi K, Wright CS, Roy S, Caruso W, Biswas RR, Iyer-Biswas S. Scaling of stochastic growth and division dynamics: A comparative study of individual rod-shaped cells in the Mother Machine and SChemostat platforms. Mol Biol Cell 2024; 35:ar78. [PMID: 38598301 DOI: 10.1091/mbc.e23-11-0452] [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: 04/12/2024] Open
Abstract
Microfluidic platforms enable long-term quantification of stochastic behaviors of individual bacterial cells under precisely controlled growth conditions. Yet, quantitative comparisons of physiological parameters and cell behaviors of different microorganisms in different experimental and device modalities is not available due to experiment-specific details affecting cell physiology. To rigorously assess the effects of mechanical confinement, we designed, engineered, and performed side-by-side experiments under otherwise identical conditions in the Mother Machine (with confinement) and the SChemostat (without confinement), using the latter as the ideal comparator. We established a protocol to cultivate a suitably engineered rod-shaped mutant of Caulobacter crescentus in the Mother Machine and benchmarked the differences in stochastic growth and division dynamics with respect to the SChemostat. While the single-cell growth rate distributions are remarkably similar, the mechanically confined cells in the Mother Machine experience a substantial increase in interdivision times. However, we find that the division ratio distribution precisely compensates for this increase, which in turn reflects identical emergent simplicities governing stochastic intergenerational homeostasis of cell sizes across device and experimental configurations, provided the cell sizes are appropriately mean-rescaled in each condition. Our results provide insights into the nature of the robustness of the bacterial growth and division machinery.
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Affiliation(s)
- Karl F Ziegler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health, Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia
| | - Kunaal Joshi
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Charles S Wright
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Shaswata Roy
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Will Caruso
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Rudro R Biswas
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Srividya Iyer-Biswas
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
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9
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Lee ST, Kuboki T, Kidoaki S, Aida Y, Arima Y, Tamada K. A plasmonic metasurface reveals differential motility of breast cancer cell lines at initial phase of adhesion. Colloids Surf B Biointerfaces 2024; 238:113876. [PMID: 38555764 DOI: 10.1016/j.colsurfb.2024.113876] [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: 01/31/2024] [Revised: 03/17/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
A plasmonic metasurface composed of a self-assembled monolayer of gold nanoparticles allows for fluorescence imaging with high spatial resolution, owing to the collective excitation of localized surface plasmon resonance. Taking advantage of fluorescence imaging confined to the nano-interface, we examined actin organization in breast cancer cell lines with different metastatic potentials during cell adhesion. Live-cell fluorescence imaging confined within tens of nanometers from the substrate shows a high actin density spanning < 1 μm from the cell edge. Live-cell imaging revealed that the breast cancer cell lines exhibited different actin patterns during the initial phase of cell adhesion (∼ 1 h). Non-tumorous MCF10A cells exhibited symmetric actin localization at the cell edge, whereas highly metastatic MDA-MB-231 cells showed asymmetric actin localization, demonstrating rapid polarization of MDA-MB-231 cells upon adhesion. The rapid actin organization observed by our plasmonic metasurface-based fluorescence imaging provides information on how quickly cancer cells sense the underlying substrate.
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Affiliation(s)
- Shi Ting Lee
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Thasaneeya Kuboki
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Satoru Kidoaki
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yukiko Aida
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yusuke Arima
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Kaoru Tamada
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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10
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Luo X, Lu Z, Jin M, Chen S, Yang J. Efficient high-resolution fluorescence projection imaging over an extended depth of field through optical hardware and deep learning optimizations. BIOMEDICAL OPTICS EXPRESS 2024; 15:3831-3847. [PMID: 38867796 PMCID: PMC11166417 DOI: 10.1364/boe.523312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/27/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024]
Abstract
Optical microscopy has witnessed notable advancements but has also become more costly and complex. Conventional wide field microscopy (WFM) has low resolution and shallow depth-of-field (DOF), which limits its applications in practical biological experiments. Recently, confocal and light sheet microscopy become major workhorses for biology that incorporate high-precision scanning to perform imaging within an extended DOF but at the sacrifice of expense, complexity, and imaging speed. Here, we propose deep focus microscopy, an efficient framework optimized both in hardware and algorithm to address the tradeoff between resolution and DOF. Our deep focus microscopy achieves large-DOF and high-resolution projection imaging by integrating a deep focus network (DFnet) into light field microscopy (LFM) setups. Based on our constructed dataset, deep focus microscopy features a significantly enhanced spatial resolution of ∼260 nm, an extended DOF of over 30 µm, and broad generalization across diverse sample structures. It also reduces the computational costs by four orders of magnitude compared to conventional LFM technologies. We demonstrate the excellent performance of deep focus microscopy in vivo, including long-term observations of cell division and migrasome formation in zebrafish embryos and mouse livers at high resolution without background contamination.
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Affiliation(s)
- Xin Luo
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Zhi Lu
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Manchang Jin
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Shuai Chen
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jingyu Yang
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
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11
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Imreh G, Hu J, Le Guyader S. Improving light microscopy training routines with evidence-based education. J Microsc 2024; 294:295-307. [PMID: 37534621 DOI: 10.1111/jmi.13216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/04/2023]
Abstract
The low reproducibility of scientific data published in articles has recently become a cause of concern in many scientific fields. Data involving light microscopy is no exception. The low awareness of researchers of the technologies they use in their research has been identified as one of the main causes of the problem. Potential solutions have hinted at the need to improve technological and methodological education within research. Despite the pivotal role of microscopy core facilities in the education of researchers being well documented, facility staff (FS) often learn their trade on the job, without receiving themselves any structured education about the technology they teach others to use. Additionally, despite endorsing an important role at the highest level of education, most FS never receive any training in pedagogy, the field of research on teaching and learning methods. In this article, we argue that the low level of awareness that researchers have of microscopy stems from a knowledge gap formed between them and microscopy FS during training routines. On the one hand, FS consider that their teaching task is to explain what is needed to produce reliable data. On the other, despite understanding what is being taught, researchers fail to learn the most challenging aspects of microscopy, those involving their judgement and reasoning. We suggest that the misunderstanding between FS and researchers is due to FS not being educated in pedagogy and thus often confusing understanding and learning. To bridge this knowledge gap and improve the quality of the microscopy education available to researchers, we propose a paradigm shift where training staff at technological core facilities be acknowledged as full-fledged teachers and offered structured education not only in the technology they teach but also in pedagogy. We then suggest that training routines at facilities be upgraded to follow the principles of the Constructive Alignment pedagogical method. We give an example of how this can be applied to existing microscopy training routines. We also describe a model to define where the responsibility of FS in training researchers begins and ends. This involves a major structural change where university staff involved in teaching research technologies themselves receive appropriate education. For this to be achieved, we advocate that funding agencies, universities, microscopy and core facility organisations mobilise resources of time and funding. Such changes may involve funding the creation and development of 'Train-the-trainer' type of courses and giving incentives for FS to upgrade their technological and pedagogical knowledge, for example by including them in career paths. We believe that this paradigm shift is necessary to improve the level of microscopy education and ultimately the reproducibility of published data.
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Affiliation(s)
- Gabriela Imreh
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jianjiang Hu
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Sylvie Le Guyader
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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12
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Jiao Z, Pan M, Yousaf K, Doveiko D, Maclean M, Griffin D, Chen Y, Li DDU. Smartphone-based optical sectioning (SOS) microscopy with a telecentric design for fluorescence imaging. J Microsc 2024. [PMID: 38808665 DOI: 10.1111/jmi.13334] [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: 10/17/2023] [Revised: 04/15/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
We propose a smartphone-based optical sectioning (SOS) microscope based on the HiLo technique, with a single smartphone replacing a high-cost illumination source and a camera sensor. We built our SOS with off-the-shelf optical, mechanical cage systems with 3D-printed adapters to seamlessly integrate the smartphone with the SOS main body. The liquid light guide can be integrated with the adapter, guiding the smartphone's LED light to the digital mirror device (DMD) with neglectable loss. We used an electrically tuneable lens (ETL) instead of a mechanical translation stage to realise low-cost axial scanning. The ETL was conjugated to the objective lens's back pupil plane (BPP) to construct a telecentric design by a 4f configuration to maintain the lateral magnification for different axial positions. SOS has a 571.5 µm telecentric scanning range and an 11.7 µm axial resolution. The broadband smartphone LED torch can effectively excite fluorescent polystyrene (PS) beads. We successfully used SOS for high-contrast fluorescent PS beads imaging with different wavelengths and optical sectioning imaging of multilayer fluorescent PS beads. To our knowledge, the proposed SOS is the first smartphone-based HiLo optical sectioning microscopy (£1965), which can save around £7035 compared with a traditional HiLo system (£9000). It is a powerful tool for biomedical research in resource-limited areas.
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Affiliation(s)
- Ziao Jiao
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Mingliang Pan
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
| | - Khadija Yousaf
- Department of Physics, University of Strathclyde, Glasgow, Scotland, UK
| | - Daniel Doveiko
- Department of Physics, University of Strathclyde, Glasgow, Scotland, UK
| | - Michelle Maclean
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
- Department of Electronic & Electrical Engineering, The Robertson Trust Laboratory for Electronic Sterilisation Technologies (ROLEST), University of Strathclyde, Glasgow, UK
| | - David Griffin
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
| | - Yu Chen
- Department of Physics, University of Strathclyde, Glasgow, Scotland, UK
| | - David Day Uei Li
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
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13
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Vicente JJ, Khan K, Tillinghast G, McFaline-Figueroa JL, Sancak Y, Stella N. The microtubule targeting agent ST-401 triggers cell death in interphase and prevents the formation of polyploid giant cancer cells. J Transl Med 2024; 22:441. [PMID: 38730481 PMCID: PMC11084142 DOI: 10.1186/s12967-024-05234-3] [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: 10/30/2023] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
Microtubule targeting agents (MTAs) are commonly prescribed to treat cancers and predominantly kill cancer cells in mitosis. Significantly, some MTA-treated cancer cells escape death in mitosis, exit mitosis and become malignant polyploid giant cancer cells (PGCC). Considering the low number of cancer cells undergoing mitosis in tumor tissues, killing them in interphase may represent a favored antitumor approach. We discovered that ST-401, a mild inhibitor of microtubule (MT) assembly, preferentially kills cancer cells in interphase as opposed to mitosis, a cell death mechanism that avoids the development of PGCC. Single cell RNA sequencing identified mRNA transcripts regulated by ST-401, including mRNAs involved in ribosome and mitochondrial functions. Accordingly, ST-401 induces a transient integrated stress response, reduces energy metabolism, and promotes mitochondria fission. This cell response may underly death in interphase and avoid the development of PGCC. Considering that ST-401 is a brain-penetrant MTA, we validated these results in glioblastoma cell lines and found that ST-401 also reduces energy metabolism and promotes mitochondria fission in GBM sensitive lines. Thus, brain-penetrant mild inhibitors of MT assembly, such as ST-401, that induce death in interphase through a previously unanticipated antitumor mechanism represent a potentially transformative new class of therapeutics for the treatment of GBM.
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Affiliation(s)
- Juan Jesus Vicente
- Department of Physiology and Biophysics, University of Washington, Health Sciences Building G424, 1705 NE Pacific Str., Seattle, WA, 98195-7280, USA.
| | - Kainat Khan
- Department of Pharmacology, University of Washington, Health Sciences Center F404A, 1959 NE Pacific Str., Seattle, WA, 98195-7280, USA
| | - Grant Tillinghast
- Department of Biomedical Engineering, Columbia University, New York, NY, 10025, USA
| | | | - Yasemin Sancak
- Department of Pharmacology, University of Washington, Health Sciences Center F404A, 1959 NE Pacific Str., Seattle, WA, 98195-7280, USA
| | - Nephi Stella
- Department of Pharmacology, University of Washington, Health Sciences Center F404A, 1959 NE Pacific Str., Seattle, WA, 98195-7280, USA.
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA.
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14
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Miyoshi T, Vishwasrao HD, Belyantseva IA, Sajeevadathan M, Ishibashi Y, Adadey SM, Harada N, Shroff H, Friedman TB. Live-cell single-molecule fluorescence microscopy for protruding organelles reveals regulatory mechanisms of MYO7A-driven cargo transport in stereocilia of inner ear hair cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.590649. [PMID: 38766013 PMCID: PMC11100596 DOI: 10.1101/2024.05.04.590649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Stereocilia are unidirectional F-actin-based cylindrical protrusions on the apical surface of inner ear hair cells and function as biological mechanosensors of sound and acceleration. Development of functional stereocilia requires motor activities of unconventional myosins to transport proteins necessary for elongating the F-actin cores and to assemble the mechanoelectrical transduction (MET) channel complex. However, how each myosin localizes in stereocilia using the energy from ATP hydrolysis is only partially understood. In this study, we develop a methodology for live-cell single-molecule fluorescence microscopy of organelles protruding from the apical surface using a dual-view light-sheet microscope, diSPIM. We demonstrate that MYO7A, a component of the MET machinery, traffics as a dimer in stereocilia. Movements of MYO7A are restricted when scaffolded by the plasma membrane and F-actin as mediated by MYO7A's interacting partners. Here, we discuss the technical details of our methodology and its future applications including analyses of cargo transportation in various organelles.
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Affiliation(s)
- Takushi Miyoshi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
- Division of Molecular and Integrative Physiology, Department of Biomedical Sciences, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA
| | - Harshad D. Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Inna A. Belyantseva
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mrudhula Sajeevadathan
- Division of Molecular and Integrative Physiology, Department of Biomedical Sciences, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA
| | - Yasuko Ishibashi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
- Inner Ear Gene Therapy Program, National Institute on Deafness and Other Communication Disorders, National Institute of Health, Bethesda, Maryland 20892, USA
| | - Samuel M. Adadey
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Narinobu Harada
- Hearing Research Laboratory, Harada ENT Clinic, Higashi-Osaka, Osaka, 577-0816, Japan
| | - Hari Shroff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Thomas B. Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
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15
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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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16
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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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17
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Garrud TAC, Bell B, Mata-Daboin A, Peixoto-Neves D, Collier DM, Cordero-Morales JF, Jaggar JH. WNK kinase is a vasoactive chloride sensor in endothelial cells. Proc Natl Acad Sci U S A 2024; 121:e2322135121. [PMID: 38568964 PMCID: PMC11009681 DOI: 10.1073/pnas.2322135121] [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: 12/21/2023] [Accepted: 03/01/2024] [Indexed: 04/05/2024] Open
Abstract
Endothelial cells (ECs) line the wall of blood vessels and regulate arterial contractility to tune regional organ blood flow and systemic pressure. Chloride (Cl-) is the most abundant anion in ECs and the Cl- sensitive With-No-Lysine (WNK) kinase is expressed in this cell type. Whether intracellular Cl- signaling and WNK kinase regulate EC function to alter arterial contractility is unclear. Here, we tested the hypothesis that intracellular Cl- signaling in ECs regulates arterial contractility and examined the signaling mechanisms involved, including the participation of WNK kinase. Our data obtained using two-photon microscopy and cell-specific inducible knockout mice indicated that acetylcholine, a prototypical vasodilator, stimulated a rapid reduction in intracellular Cl- concentration ([Cl-]i) due to the activation of TMEM16A, a Cl- channel, in ECs of resistance-size arteries. TMEM16A channel-mediated Cl- signaling activated WNK kinase, which phosphorylated its substrate proteins SPAK and OSR1 in ECs. OSR1 potentiated transient receptor potential vanilloid 4 (TRPV4) currents in a kinase-dependent manner and required a conserved binding motif located in the channel C terminus. Intracellular Ca2+ signaling was measured in four dimensions in ECs using a high-speed lightsheet microscope. WNK kinase-dependent activation of TRPV4 channels increased local intracellular Ca2+ signaling in ECs and produced vasodilation. In summary, we show that TMEM16A channel activation reduces [Cl-]i, which activates WNK kinase in ECs. WNK kinase phosphorylates OSR1 which then stimulates TRPV4 channels to produce vasodilation. Thus, TMEM16A channels regulate intracellular Cl- signaling and WNK kinase activity in ECs to control arterial contractility.
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Affiliation(s)
- Tessa A. C. Garrud
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN38163
| | - Briar Bell
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN38163
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX77030
| | - Alejandro Mata-Daboin
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN38163
| | | | - Daniel M. Collier
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN38163
| | - Julio F. Cordero-Morales
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN38163
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX77030
| | - Jonathan H. Jaggar
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN38163
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18
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Brückner DB, Broedersz CP. Learning dynamical models of single and collective cell migration: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:056601. [PMID: 38518358 DOI: 10.1088/1361-6633/ad36d2] [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: 10/07/2023] [Accepted: 03/22/2024] [Indexed: 03/24/2024]
Abstract
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical perspective, a broad variety of models for the underlying physical mechanisms that govern cell motility have been developed. A key challenge in the development of such models is how to connect them to experimental observations, which often exhibit complex stochastic behaviours. In this review, we discuss recent advances in data-driven theoretical approaches that directly connect with experimental data to infer dynamical models of stochastic cell migration. Leveraging advances in nanofabrication, image analysis, and tracking technology, experimental studies now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical efforts have been directed towards integrating such datasets into physical models from the single cell to the tissue scale with the aim of conceptualising the emergent behaviour of cells. We first review how this inference problem has been addressed in both freely migrating and confined cells. Next, we discuss why these dynamics typically take the form of underdamped stochastic equations of motion, and how such equations can be inferred from data. We then review applications of data-driven inference and machine learning approaches to heterogeneity in cell behaviour, subcellular degrees of freedom, and to the collective dynamics of multicellular systems. Across these applications, we emphasise how data-driven methods can be integrated with physical active matter models of migrating cells, and help reveal how underlying molecular mechanisms control cell behaviour. Together, these data-driven approaches are a promising avenue for building physical models of cell migration directly from experimental data, and for providing conceptual links between different length-scales of description.
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Affiliation(s)
- David B Brückner
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Chase P Broedersz
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilian-University Munich, Theresienstr. 37, D-80333 Munich, Germany
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19
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Quinsgaard EMB, Korsnes MS, Korsnes R, Moestue SA. Single-cell tracking as a tool for studying EMT-phenotypes. Exp Cell Res 2024; 437:113993. [PMID: 38485079 DOI: 10.1016/j.yexcr.2024.113993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/24/2024]
Abstract
This article demonstrates that label-free single-cell video tracking is a useful approach for in vitro studies of Epithelial-Mesenchymal Transition (EMT). EMT is a highly heterogeneous process, involved in wound healing, embryogenesis and cancer. The process promotes metastasis, and increased understanding can aid development of novel therapeutic strategies. The role of EMT-associated biomarkers depends on biological context, making it challenging to compare and interpret data from different studies. We demonstrate single-cell video tracking for comprehensive phenotype analysis. In this study we performed single-cell video tracking on 72-h long recordings. We quantified several behaviours at a single-cell level during induced EMT in MDA-MB-468 cells. This revealed notable variations in migration speed, with different dose-response patterns and varying distributions of speed. By registering cell morphologies during the recording, we determined preferred paths of morphological transitions. We also found a clear association between migration speed and cell morphology. We found elevated rates of cell death, diminished proliferation, and an increase in mitotic failures followed by re-fusion of sister-cells. The method allows tracking of phenotypes in cell lineages, which can be particularly useful in epigenetic studies. Sister-cells were found to have significant similarities in their speeds and morphologies, illustrating the heritability of these traits.
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Affiliation(s)
- Ellen Marie Botne Quinsgaard
- Norwegian University of Science and Technology (NTNU), Department of Clinical and Molecular Medicine, NO-7491 Trondheim, Norway.
| | - Mónica Suárez Korsnes
- Norwegian University of Science and Technology (NTNU), Department of Clinical and Molecular Medicine, NO-7491 Trondheim, Norway; Korsnes Biocomputing (KoBio), Trondheim, Norway
| | | | - Siver Andreas Moestue
- Norwegian University of Science and Technology (NTNU), Department of Clinical and Molecular Medicine, NO-7491 Trondheim, Norway; Department of Pharmacy, Nord University, Bodø, Norway
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20
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O’Callaghan P, Idevall-Hagren O. "Blue Light, Camera, Action!". ACS CENTRAL SCIENCE 2024; 10:514-516. [PMID: 38559309 PMCID: PMC10979495 DOI: 10.1021/acscentsci.4c00317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Affiliation(s)
- Paul O’Callaghan
- Department of Medical Cell Biology, Uppsala University, Uppsala 75123, Sweden
| | - Olof Idevall-Hagren
- Department of Medical Cell Biology, Uppsala University, Uppsala 75123, Sweden
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21
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Ren X, Wang C, Wu X, Rong M, Huang R, Liang Q, Shen T, Sun H, Zhang R, Zhang Z, Liu X, Song X, Foley JW. Auxochrome Dimethyl-Dihydroacridine Improves Fluorophores for Prolonged Live-Cell Super-Resolution Imaging. J Am Chem Soc 2024; 146:6566-6579. [PMID: 38422385 DOI: 10.1021/jacs.3c11823] [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: 03/02/2024]
Abstract
Superior photostability, minimal phototoxicity, red-shifted absorption/emission wavelengths, high brightness, and an enlarged Stokes shift are essential characteristics of top-tier organic fluorophores, particularly for long-lasting super-resolution imaging in live cells (e.g., via stimulated emission depletion (STED) nanoscopy). However, few existing fluorophores possess all of these properties. In this study, we demonstrate a general approach for simultaneously enhancing these parameters through the introduction of 9,9-dimethyl-9,10-dihydroacridine (DMA) as an electron-donating auxochrome. DMA not only induces red shifts in emission wavelengths but also suppresses photooxidative reactions and prevents the formation of triplet states in DMA-based fluorophores, greatly improving photostability and remarkably minimizing phototoxicity. Moreover, the DMA group enhances the fluorophores' brightness and enlarges the Stokes shift. Importantly, the "universal" benefits of attaching the DMA auxochrome have been exemplified in various fluorophores including rhodamines, difluoride-boron complexes, and coumarin derivatives. The resulting fluorophores successfully enabled the STED imaging of organelles and HaloTag-labeled membrane proteins.
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Affiliation(s)
- Xiaojie Ren
- College of Chemistry & Chemical Engineering, Central South University, Changsha 410083, Hunan, China
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Chao Wang
- Singapore University of Technology and Design, 8 Somapah Road, 487372 Singapore
| | - Xia Wu
- Singapore University of Technology and Design, 8 Somapah Road, 487372 Singapore
| | - Mengtao Rong
- School of Chemistry and Chemical Engineering, Anhui University, Hefei 230601, Anhui, China
| | - Rong Huang
- College of Chemistry & Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Qin Liang
- College of Chemistry & Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Tianruo Shen
- Singapore University of Technology and Design, 8 Somapah Road, 487372 Singapore
| | - Hongyan Sun
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Ruilong Zhang
- School of Chemistry and Chemical Engineering, Anhui University, Hefei 230601, Anhui, China
| | - Zhongping Zhang
- School of Chemistry and Chemical Engineering, Anhui University, Hefei 230601, Anhui, China
| | - Xiaogang Liu
- Singapore University of Technology and Design, 8 Somapah Road, 487372 Singapore
| | - Xiangzhi Song
- College of Chemistry & Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - James W Foley
- Rowland Institute at Harvard, Harvard University, Boston, Massachusetts 02142, United States
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22
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Dukhno O, Ghosh S, Greiner V, Bou S, Godet J, Muhr V, Buchner M, Hirsch T, Mély Y, Przybilla F. Targeted Single Particle Tracking with Upconverting Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2024; 16:11217-11227. [PMID: 38386424 DOI: 10.1021/acsami.3c17116] [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: 02/24/2024]
Abstract
Single particle tracking (SPT) is a powerful technique for real-time microscopic visualization of the movement of individual biomolecules within or on the surface of living cells. However, SPT often suffers from the suboptimal performance of the photon-emitting labels used to tag the biomolecules of interest. For example, fluorescent dyes have poor photostability, while quantum dots suffer from blinking that hampers track acquisition and interpretation. Upconverting nanoparticles (UCNPs) have recently emerged as a promising anti-Stokes luminescent label for SPT. In this work, we demonstrated targeted SPT using UCNPs. For this, we synthesized 30 nm diameter doped UCNPs and coated them with amphiphilic polymers decorated with polyethylene glycol chains to make them water-dispersible and minimize their nonspecific interactions with cells. Coated UCNPs highly homogeneous in brightness (as confirmed by a single particle investigation) were functionalized by immunoglobulin E (IgE) using a biotin-streptavidin strategy. Using these IgE-UCNP SPT labels, we tracked high-affinity IgE receptors (FcεRI) on the membrane of living RBL-2H3 mast cells at 37 °C in the presence and absence of antigen and obtained good agreement with the literature. Moreover, we used the FcεRI-IgE receptor-antibody system to directly compare the performance of UCNP-based SPT labels to organic dyes (AlexaFluor647) and quantum dots (QD655). Due to their photostability as well as their backgroundless and continuous luminescence, SPT trajectories obtained with UCNP labels are no longer limited by the photophysics of the label but only by the dynamics of the system and, in particular, the movement of the label out of the field of view and/or focal plane.
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Affiliation(s)
- Oleksii Dukhno
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Srijayee Ghosh
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Vanille Greiner
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Sophie Bou
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Julien Godet
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
- IMAGeS team at ICube, UMR 7357, CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Verena Muhr
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
| | - Markus Buchner
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
| | - Thomas Hirsch
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
| | - Yves Mély
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Frédéric Przybilla
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
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23
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Cui M, Lee S, Ban SH, Ryu JR, Shen M, Yang SH, Kim JY, Choi SK, Han J, Kim Y, Han K, Lee D, Sun W, Kwon HB, Lee D. A single-component, light-assisted uncaging switch for endoproteolytic release. Nat Chem Biol 2024; 20:353-364. [PMID: 37973890 DOI: 10.1038/s41589-023-01480-6] [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: 05/06/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Proteases function as pivotal molecular switches, initiating numerous biological events. Notably, potyviral protease, derived from plant viruses, has emerged as a trusted proteolytic switch in synthetic biological circuits. To harness their capabilities, we have developed a single-component photocleavable switch, termed LAUNCHER (Light-Assisted UNcaging switCH for Endoproteolytic Release), by employing a circularly permutated tobacco etch virus protease and a blue-light-gated substrate, which are connected by fine-tuned intermodular linkers. As a single-component system, LAUNCHER exhibits a superior signal-to-noise ratio compared with multi-component systems, enabling precise and user-controllable release of payloads. This characteristic renders LAUNCHER highly suitable for diverse cellular applications, including transgene expression, tailored subcellular translocation and optochemogenetics. Additionally, the plug-and-play integration of LAUNCHER into existing synthetic circuits facilitates the enhancement of circuit performance. The demonstrated efficacy of LAUNCHER in improving existing circuitry underscores its significant potential for expanding its utilization in various applications.
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Affiliation(s)
- Mingguang Cui
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seunghwan Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sung Hwan Ban
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jae Ryun Ryu
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Meiying Shen
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Hyun Yang
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Young Kim
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seul Ki Choi
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jaemin Han
- Korea University College of Medicine, Seoul, Republic of Korea
| | - Yoonhee Kim
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kihoon Han
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Donghun Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyung-Bae Kwon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dongmin Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.
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24
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Verrier N, Debailleul M, Haeberlé O. Recent Advances and Current Trends in Transmission Tomographic Diffraction Microscopy. SENSORS (BASEL, SWITZERLAND) 2024; 24:1594. [PMID: 38475130 DOI: 10.3390/s24051594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024]
Abstract
Optical microscopy techniques are among the most used methods in biomedical sample characterization. In their more advanced realization, optical microscopes demonstrate resolution down to the nanometric scale. These methods rely on the use of fluorescent sample labeling in order to break the diffraction limit. However, fluorescent molecules' phototoxicity or photobleaching is not always compatible with the investigated samples. To overcome this limitation, quantitative phase imaging techniques have been proposed. Among these, holographic imaging has demonstrated its ability to image living microscopic samples without staining. However, for a 3D assessment of samples, tomographic acquisitions are needed. Tomographic Diffraction Microscopy (TDM) combines holographic acquisitions with tomographic reconstructions. Relying on a 3D synthetic aperture process, TDM allows for 3D quantitative measurements of the complex refractive index of the investigated sample. Since its initial proposition by Emil Wolf in 1969, the concept of TDM has found a lot of applications and has become one of the hot topics in biomedical imaging. This review focuses on recent achievements in TDM development. Current trends and perspectives of the technique are also discussed.
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Affiliation(s)
- Nicolas Verrier
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, 68093 Mulhouse, France
| | - Matthieu Debailleul
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, 68093 Mulhouse, France
| | - Olivier Haeberlé
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, 68093 Mulhouse, France
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25
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Asmar AJ, Benson ZA, Peskin AP, Chalfoun J, Simon M, Halter M, Plant AL. High-volume, label-free imaging for quantifying single-cell dynamics in induced pluripotent stem cell colonies. PLoS One 2024; 19:e0298446. [PMID: 38377138 PMCID: PMC10878516 DOI: 10.1371/journal.pone.0298446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
To facilitate the characterization of unlabeled induced pluripotent stem cells (iPSCs) during culture and expansion, we developed an AI pipeline for nuclear segmentation and mitosis detection from phase contrast images of individual cells within iPSC colonies. The analysis uses a 2D convolutional neural network (U-Net) plus a 3D U-Net applied on time lapse images to detect and segment nuclei, mitotic events, and daughter nuclei to enable tracking of large numbers of individual cells over long times in culture. The analysis uses fluorescence data to train models for segmenting nuclei in phase contrast images. The use of classical image processing routines to segment fluorescent nuclei precludes the need for manual annotation. We optimize and evaluate the accuracy of automated annotation to assure the reliability of the training. The model is generalizable in that it performs well on different datasets with an average F1 score of 0.94, on cells at different densities, and on cells from different pluripotent cell lines. The method allows us to assess, in a non-invasive manner, rates of mitosis and cell division which serve as indicators of cell state and cell health. We assess these parameters in up to hundreds of thousands of cells in culture for more than 36 hours, at different locations in the colonies, and as a function of excitation light exposure.
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Affiliation(s)
- Anthony J. Asmar
- Biosystems and Biomaterials Division Material Measurement Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Zackery A. Benson
- Biosystems and Biomaterials Division Material Measurement Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Adele P. Peskin
- Software and Systems Division Information Technology Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Joe Chalfoun
- Software and Systems Division Information Technology Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Mylene Simon
- Software and Systems Division Information Technology Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Michael Halter
- Biosystems and Biomaterials Division Material Measurement Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Anne L. Plant
- Biosystems and Biomaterials Division Material Measurement Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
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26
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Inavalli VVGK, Puente Muñoz V, Draffin JE, Tønnesen J. Fluorescence microscopy shadow imaging for neuroscience. Front Cell Neurosci 2024; 18:1330100. [PMID: 38425431 PMCID: PMC10902105 DOI: 10.3389/fncel.2024.1330100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Fluorescence microscopy remains one of the single most widely applied experimental approaches in neuroscience and beyond and is continuously evolving to make it easier and more versatile. The success of the approach is based on synergistic developments in imaging technologies and fluorophore labeling strategies that have allowed it to greatly diversify and be used across preparations for addressing structure as well as function. Yet, while targeted labeling strategies are a key strength of fluorescence microscopy, they reciprocally impose general limitations on the possible types of experiments and analyses. One recent development that overcomes some of these limitations is fluorescence microscopy shadow imaging, where membrane-bound cellular structures remain unlabeled while the surrounding extracellular space is made to fluoresce to provide a negative contrast shadow image. When based on super-resolution STED microscopy, the technique in effect provides a positive image of the extracellular space geometry and entire neuropil in the field of view. Other noteworthy advantages include the near elimination of the adverse effects of photobleaching and toxicity in live imaging, exhaustive and homogeneous labeling across the preparation, and the ability to apply and adjust the label intensity on the fly. Shadow imaging is gaining popularity and has been applied on its own or combined with conventional positive labeling to visualize cells and synaptic proteins in their parenchymal context. Here, we highlight the inherent limitations of fluorescence microscopy and conventional labeling and contrast these against the pros and cons of recent shadow imaging approaches. Our aim is to describe the brief history and current trajectory of the shadow imaging technique in the neuroscience field, and to draw attention to its ease of application and versatility.
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Affiliation(s)
| | - Virginia Puente Muñoz
- Department of Neurosciences, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Jonathan E. Draffin
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
- Aligning Science Across Parkinson’s (ASAP), Collaborative Research Network, Chevy Chase, MD, United States
| | - Jan Tønnesen
- Department of Neurosciences, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
- Aligning Science Across Parkinson’s (ASAP), Collaborative Research Network, Chevy Chase, MD, United States
- Instituto Biofisika (CSIC/UPV), Leioa, Spain
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27
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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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28
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Gritti N, Power RM, Graves A, Huisken J. Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging. Nat Methods 2024; 21:311-321. [PMID: 38177507 PMCID: PMC10864180 DOI: 10.1038/s41592-023-02127-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 11/10/2023] [Indexed: 01/06/2024]
Abstract
Time-lapse fluorescence microscopy is key to unraveling biological development and function; however, living systems, by their nature, permit only limited interrogation and contain untapped information that can only be captured by more invasive methods. Deep-tissue live imaging presents a particular challenge owing to the spectral range of live-cell imaging probes/fluorescent proteins, which offer only modest optical penetration into scattering tissues. Herein, we employ convolutional neural networks to augment live-imaging data with deep-tissue images taken on fixed samples. We demonstrate that convolutional neural networks may be used to restore deep-tissue contrast in GFP-based time-lapse imaging using paired final-state datasets acquired using near-infrared dyes, an approach termed InfraRed-mediated Image Restoration (IR2). Notably, the networks are remarkably robust over a wide range of developmental times. We employ IR2 to enhance the information content of green fluorescent protein time-lapse images of zebrafish and Drosophila embryo/larval development and demonstrate its quantitative potential in increasing the fidelity of cell tracking/lineaging in developing pescoids. Thus, IR2 is poised to extend live imaging to depths otherwise inaccessible.
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Affiliation(s)
- Nicola Gritti
- Morgridge Institute for Research, Madison, WI, USA
- Mesoscopic Imaging Facility, European Molecular Biology Laboratory Barcelona, Barcelona, Spain
| | - Rory M Power
- Morgridge Institute for Research, Madison, WI, USA
- EMBL Imaging Center, European Molecular Biology Laboratory Heidelberg, Heidelberg, Germany
| | | | - Jan Huisken
- Morgridge Institute for Research, Madison, WI, USA.
- Department of Integrative Biology, University of Wisconsin Madison, Madison, WI, USA.
- Department of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
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29
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Muhammed Y, Lazenby RA. Scanning ion conductance microscopy revealed cisplatin-induced morphological changes related to apoptosis in single adenocarcinoma cells. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:503-514. [PMID: 38167666 DOI: 10.1039/d3ay01827j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The studies of drug-induced apoptosis play a vital role in the identification of potential drugs that could treat diseases such as cancer. Alterations in the native morphology of cancer cells following treatment with anticancer drugs serve as one of the indicators that reveal drug efficacy. Various techniques such as optical microscopy, electron microscopy (EM), and atomic force microscopy (AFM) have been used to map the three dimensional (3D) morphological changes in cells induced with drugs. However, caution should be exercised when interpreting morphological data from techniques that might alter the native morphology of cells, caused by phototoxicity, electron beam invasiveness, intrusive sample preparation, and cell membrane deformation. Herein, we have used scanning ion conductance microscopy (SICM) to study the 3D morphology and roughness of A549 adenocarcinoma cells under physiological conditions before and after cisplatin induced apoptosis, where we observed an increase in height, overall shrinkage of the cells, and irregular features form on the cell membrane. Tracking the morphology of the same single A549 cells exposed to cisplatin unveiled heterogeneity in response to the drug, formation of membrane blebs, and an increase in membrane roughness. We have also demonstrated the use of SICM for studying the effect of cisplatin on the dynamic changes in the volume of A549 cells over days. SICM is demonstrated as a technique for studying the effect of drug induced apoptosis in the same cells over time, and for multiple different single cells.
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Affiliation(s)
- Yusuf Muhammed
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, USA.
| | - Robert A Lazenby
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, USA.
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30
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Mahapatra S, Ma S, Dong B, Zhang C. Quantification of cellular phototoxicity of organelle stains by the dynamics of microtubule polymerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576021. [PMID: 38293099 PMCID: PMC10827188 DOI: 10.1101/2024.01.17.576021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Being able to quantify the phototoxicity of dyes and drugs in live cells allows biologists to better understand cell responses to exogenous stimuli during imaging. This capability further helps to design fluorescent labels with lower phototoxicity and drugs with better efficacy. Conventional ways to evaluate cellular phototoxicity rely on late-stage measurements of individual or different populations of cells. Here, we developed a quantitative method using intracellular microtubule polymerization as a rapid and sensitive marker to quantify early-stage phototoxicity. Implementing this method, we assessed the photosensitization induced by organelle dyes illuminated with different excitation wavelengths. Notably, fluorescent markers targeting mitochondria, nuclei, and endoplasmic reticulum exhibited diverse levels of phototoxicity. Furthermore, leveraging a real-time precision opto-control technology allowed us to evaluate the synergistic effect of light and dyes on specific organelles. Studies in hypoxia revealed enhanced phototoxicity of Mito-Tracker Red CMXRos that is not correlated with the generation of reactive oxygen species but a different deleterious pathway in low oxygen conditions. Teaser Microtubule dynamics in live cells allow quantification of cellular phototoxicity of fluorescent dyes in various conditions.
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31
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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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32
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Minami SA, Garimella SS, Shah PS. Computational evaluation of light propagation in cylindrical bioreactors for optogenetic mammalian cell cultures. Biotechnol J 2024; 19:e2300071. [PMID: 37877211 DOI: 10.1002/biot.202300071] [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: 02/14/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/26/2023]
Abstract
Light-inducible regulation of cellular pathways and gene circuits in mammalian cells is a new frontier in mammalian genetic engineering. Optogenetic mammalian cell cultures, which are light-sensitive engineered cells, utilize light to regulate gene expression and protein activity. As a low-cost, tunable, and reversible input, light is highly adept at spatiotemporal and orthogonal regulation of cellular behavior. However, light is absorbed and scattered as it travels through media and cells, and the applicability of optogenetics in larger mammalian bioreactors has not been determined. In this work, we computationally explore the size limit to which optogenetics can be applied in cylindrical bioreactors at relevant height-to-diameter ratios. We model the propagation of light using the radiative transfer equation and consider changes in reactor volume, absorption coefficient, scattering coefficient, and scattering anisotropy. We observe sufficient light penetration for activation in simulated bioreactors with sizes of up to 80,000 L at maximal cell densities. We performed supporting experiments and found that significant attenuation occurs at the boundaries of the system, but the relative change in intensity distribution within the reactor was consistent with simulation results. We conclude that optogenetics can be applied to bioreactors at an industrial scale and may be a valuable tool for specific biomanufacturing applications.
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Affiliation(s)
- Shiaki A Minami
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Shruthi S Garimella
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Priya S Shah
- Department of Chemical Engineering, University of California, Davis, California, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA
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33
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Allroggen N, Breuer H, Bachmann S, Bell M, Zempel H. Studying Microtubule Dynamics in Human Neurons: Two-Dimensional Microtubule Tracing and Kymographs in iPSC- and SH-SY5Y-Derived Neurons for Tau Research. Methods Mol Biol 2024; 2754:561-580. [PMID: 38512690 DOI: 10.1007/978-1-0716-3629-9_33] [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: 03/23/2024]
Abstract
The study of microtubule (MT) dynamics is essential for the understanding of cellular transport, cell polarity, axon formation, and other neurodevelopmental mechanisms. All these processes rely on the constant transition between assembly and disassembly of tubulin polymers to/from MTs, known as dynamic instability. This process is well-regulated, among others, by phosphorylation of microtubule-associated proteins (MAP), including the Tau protein. Protein kinases, in particular the microtubule affinity regulating kinase (MARK), regulate the MT-Tau interaction, inducing Tau dissociation by phosphorylation. Phosphorylated Tau dissociates from microtubules forming insoluble aggregates known as neurofibrillary tangles. These accumulations of hyperphosphorylated Tau in the neurons disrupt the physiological MT-based transport machinery within the cell and can potentially lead to the development of neurodegenerative disorders, such as Alzheimer's disease (AD) and related tauopathies. Further investigations on the MT cytoskeleton dynamics are essential as they may elucidate pathomechanisms of neurodegenerative diseases - particularly tauopathies - as well as fundamental neurodevelopmental processes.The study of the dynamic assembly and disassembly of the MT network requires live-cell imaging rather than conventional immunocytochemistry based on fixed samples. To investigate MT dynamics, we perform live-cell imaging of neurons transfected with a fluorescently tagged version of the microtubule plus-end tracking protein (+TIP) EB3. This protein associates with the growing ends of MTs and thus visualizes MT growth in real time. Our imaging analysis protocol allows the determination of quantity, orientation, and velocity of MT growth in the soma and neurites of transfected neurons, using ImageJ-based tracking software and kymographs. Furthermore, functional effects of Tau and MARK kinases on the MT cytoskeleton can be assessed by overexpression or downregulation experiments of the respective protein prior to the live imaging assay. We use two different human neuronal cell models, naive and differentiated SH-SY5Y neuroblastoma cells, and neurons derived from induced pluripotent stem cells (iPSCs), both of which have shown success as models to study Tau-related pathologies.This protocol describes an optimized method for analysis of microtubule dynamics using fluorescent tagged EB3 protein as microtubule plus end marker. In this chapter, we outline the process of neuronal transfection, live-cell imaging, and necessary time-lapse image analysis based on ImageJ in two human-derived neuronal systems, which are suitable for the analysis of Tau trafficking and sorting studies.
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Affiliation(s)
- Nadine Allroggen
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Helen Breuer
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Sarah Bachmann
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Michael Bell
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Hans Zempel
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
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Ortiz-Perez A, Zhang M, Fitzpatrick LW, Izquierdo-Lozano C, Albertazzi L. Advanced optical imaging for the rational design of nanomedicines. Adv Drug Deliv Rev 2024; 204:115138. [PMID: 37980951 DOI: 10.1016/j.addr.2023.115138] [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: 06/09/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Abstract
Despite the enormous potential of nanomedicines to shape the future of medicine, their clinical translation remains suboptimal. Translational challenges are present in every step of the development pipeline, from a lack of understanding of patient heterogeneity to insufficient insights on nanoparticle properties and their impact on material-cell interactions. Here, we discuss how the adoption of advanced optical microscopy techniques, such as super-resolution optical microscopies, correlative techniques, and high-content modalities, could aid the rational design of nanocarriers, by characterizing the cell, the nanomaterial, and their interaction with unprecedented spatial and/or temporal detail. In this nanomedicine arena, we will discuss how the implementation of these techniques, with their versatility and specificity, can yield high volumes of multi-parametric data; and how machine learning can aid the rapid advances in microscopy: from image acquisition to data interpretation.
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Affiliation(s)
- Ana Ortiz-Perez
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Miao Zhang
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Laurence W Fitzpatrick
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Cristina Izquierdo-Lozano
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
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Celinskis D, Black CJ, Murphy J, Barrios-Anderson A, Friedman N, Shaner NC, Saab C, Gomez-Ramirez M, Lipscombe D, Borton DA, Moore CI. Towards a Brighter Constellation: Multi-Organ Neuroimaging of Neural and Vascular Dynamics in the Spinal Cord and Brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.25.573323. [PMID: 38234789 PMCID: PMC10793404 DOI: 10.1101/2023.12.25.573323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Significance Pain is comprised of a complex interaction between motor action and somatosensation that is dependent on dynamic interactions between the brain and spinal cord. This makes understanding pain particularly challenging as it involves rich interactions between many circuits (e.g., neural and vascular) and signaling cascades throughout the body. As such, experimentation on a single region may lead to an incomplete and potentially incorrect understanding of crucial underlying mechanisms. Aim Here, we aimed to develop and validate new tools to enable detailed and extended observation of neural and vascular activity in the brain and spinal cord. The first key set of innovations were targeted to developing novel imaging hardware that addresses the many challenges of multi-site imaging. The second key set of innovations were targeted to enabling bioluminescent imaging, as this approach can address limitations of fluorescent microscopy including photobleaching, phototoxicity and decreased resolution due to scattering of excitation signals. Approach We designed 3D-printed brain and spinal cord implants to enable effective surgical implantations and optical access with wearable miniscopes or an open window (e.g., for one- or two-photon microscopy or optogenetic stimulation). We also tested the viability for bioluminescent imaging, and developed a novel modified miniscope optimized for these signals (BLmini). Results Here, we describe novel 'universal' implants for acute and chronic simultaneous brain-spinal cord imaging and optical stimulation. We further describe successful imaging of bioluminescent signals in both foci, and a new miniscope, the 'BLmini,' which has reduced weight, cost and form-factor relative to standard wearable miniscopes. Conclusions The combination of 3D printed implants, advanced imaging tools, and bioluminescence imaging techniques offers a new coalition of methods for understanding spinal cord-brain interactions. This work has the potential for use in future research into neuropathic pain and other sensory disorders and motor behavior.
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Affiliation(s)
| | | | - Jeremy Murphy
- Carney Institute for Brain Science, Providence, RI, USA
| | | | - Nina Friedman
- Carney Institute for Brain Science, Providence, RI, USA
| | - Nathan C. Shaner
- University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Carl Saab
- Cleveland Clinic Lerner Research Institute, Department of Biomedical Engineering and Neurological Institute, Cleveland, OH, USA
| | | | | | - David A. Borton
- Carney Institute for Brain Science, Providence, RI, USA
- School of Engineering, Brown University, RI, USA
- Center for Neurorestoration and Neurotechnology, Providence VA Medical Center, RI, USA
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36
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Holme B, Bjørnerud B, Pedersen NM, de la Ballina LR, Wesche J, Haugsten EM. Automated tracking of cell migration in phase contrast images with CellTraxx. Sci Rep 2023; 13:22982. [PMID: 38151514 PMCID: PMC10752880 DOI: 10.1038/s41598-023-50227-9] [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: 07/13/2023] [Accepted: 12/17/2023] [Indexed: 12/29/2023] Open
Abstract
The ability of cells to move and migrate is required during development, but also in the adult in processes such as wound healing and immune responses. In addition, cancer cells exploit the cells' ability to migrate and invade to spread into nearby tissue and eventually metastasize. The majority of cancer deaths are caused by metastasis and the process of cell migration is therefore intensively studied. A common way to study cell migration is to observe cells through an optical microscope and record their movements over time. However, segmenting and tracking moving cells in phase contrast time-lapse video sequences is a challenging task. Several tools to track the velocity of migrating cells have been developed. Unfortunately, most of the automated tools are made for fluorescence images even though unlabelled cells are often preferred to avoid phototoxicity. Consequently, researchers are constrained with laborious manual tracking tools using ImageJ or similar software. We have therefore developed a freely available, user-friendly, automated tracking tool called CellTraxx. This software makes it easy to measure the velocity and directness of migrating cells in phase contrast images. Here, we demonstrate that our tool efficiently recognizes and tracks unlabelled cells of different morphologies and sizes (HeLa, RPE1, MDA-MB-231, HT1080, U2OS, PC-3) in several types of cell migration assays (random migration, wound healing and cells embedded in collagen). We also provide a detailed protocol and download instructions for CellTraxx.
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Affiliation(s)
- Børge Holme
- SINTEF Industry, Forskningsveien 1, 0373, Oslo, Norway
| | - Birgitte Bjørnerud
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Montebello, 0379, Oslo, Norway
| | - Nina Marie Pedersen
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Montebello, 0379, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
- Department of Nursing, Health and Laboratory Science, Faculty of Health, Welfare and Organisation, Østfold University College, PB 700, NO-1757, Halden, Norway
| | - Laura Rodriguez de la Ballina
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Montebello, 0379, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Jørgen Wesche
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Montebello, 0379, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372, Oslo, Norway
| | - Ellen Margrethe Haugsten
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway.
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Montebello, 0379, Oslo, Norway.
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37
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Sardana J, Devinder S, Zhu W, Agrawal A, Joseph J. Dielectric Metasurface Enabled Compact, Single-Shot Digital Holography for Quantitative Phase Imaging. NANO LETTERS 2023. [PMID: 38037916 DOI: 10.1021/acs.nanolett.3c03515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Quantitative phase imaging (QPI) enables nondestructive, real-time, label-free imaging of transparent specimens and can reveal information about their fundamental properties such as cell size and morphology, mass density, particle dynamics, and cellular fluctuations. Development of high-performance and low-cost quantitative phase imaging systems is thus required in many fields, including on-site biomedical imaging and industrial inspection. Here, we propose an ultracompact, highly stable interferometer based on a single-layer dielectric metasurface for common path off-axis digital holography and experimentally demonstrate quantitative phase imaging. The interferometric imaging system leveraging an ultrathin multifunctional metasurface captures image plane holograms in a single shot and provides quantitative phase information on the test samples for extraction of its physical properties. With the benefits of planar engineering and high integrability, the proposed metasurface-based method establishes a stable miniaturized QPI system for reliable and cost-effective point-of-care devices, live cell imaging, 3D topography, and edge detection for optical computing.
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Affiliation(s)
- Jyoti Sardana
- Department of Physics, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shital Devinder
- Centre for Sensors, Instrumentation and Cyber Physical System Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Wenqi Zhu
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Amit Agrawal
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Joby Joseph
- Department of Physics, Indian Institute of Technology Delhi, New Delhi 110016, India
- Centre for Sensors, Instrumentation and Cyber Physical System Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
- Optics and Photonics Center, Indian Institute of Technology Delhi, New Delhi 110016, India
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38
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Last MGF, Noteborn WEM, Voortman LM, Sharp TH. Super-resolution fluorescence imaging of cryosamples does not limit achievable resolution in cryoEM. J Struct Biol 2023; 215:108040. [PMID: 37918761 DOI: 10.1016/j.jsb.2023.108040] [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: 03/20/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Correlated super-resolution cryo-fluorescence and cryo-electron microscopy (cryoEM) has been gaining popularity as a method to investigate biological samples with high resolution and specificity. A concern in this combined method (called SR-cryoCLEM), however, is whether and how fluorescence imaging prior to cryoEM acquisition is detrimental to sample integrity. In this report, we investigated the effect of high-dose laser light (405, 488, and 561 nm) irradiation on apoferritin samples prepared for cryoEM with excitation wavelengths commonly used in fluorescence microscopy, and compared these samples to controls that were kept in the dark. We found that laser illumination, of equal duration and intensity as used in cryo-single molecule localization microscopy (cryoSMLM) and in the presence of high concentrations of fluorescent protein, did not affect the achievable resolution in cryoEM, with final reconstructions reaching resolutions of ∼ 1.8 Å regardless of the laser illumination. The finding that super-resolution fluorescence imaging of cryosamples prior to cryoEM data acquisition does not limit the achievable resolution suggests that super-resolution cryo-fluorescence microscopy and in situ structural biology using cryoEM are entirely compatible.
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Affiliation(s)
- Mart G F Last
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Willem E M Noteborn
- Netherlands Centre for Electron Nanoscopy, Leiden University, 2333 AL Leiden, The Netherlands
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands.
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39
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Pylvänäinen JW, Gómez-de-Mariscal E, Henriques R, Jacquemet G. Live-cell imaging in the deep learning era. Curr Opin Cell Biol 2023; 85:102271. [PMID: 37897927 DOI: 10.1016/j.ceb.2023.102271] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/30/2023]
Abstract
Live imaging is a powerful tool, enabling scientists to observe living organisms in real time. In particular, when combined with fluorescence microscopy, live imaging allows the monitoring of cellular components with high sensitivity and specificity. Yet, due to critical challenges (i.e., drift, phototoxicity, dataset size), implementing live imaging and analyzing the resulting datasets is rarely straightforward. Over the past years, the development of bioimage analysis tools, including deep learning, is changing how we perform live imaging. Here we briefly cover important computational methods aiding live imaging and carrying out key tasks such as drift correction, denoising, super-resolution imaging, artificial labeling, tracking, and time series analysis. We also cover recent advances in self-driving microscopy.
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Affiliation(s)
- Joanna W Pylvänäinen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi, University, 20520 Turku, Finland
| | | | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal; University College London, London WC1E 6BT, United Kingdom
| | - Guillaume Jacquemet
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi, University, 20520 Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Turku Bioimaging, University of Turku and Åbo Akademi University, FI- 20520 Turku, Finland.
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40
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Lahlou A, Tehrani HS, Coghill I, Shpinov Y, Mandal M, Plamont MA, Aujard I, Niu Y, Nedbal L, Lazár D, Mahou P, Supatto W, Beaurepaire E, Eisenmann I, Desprat N, Croquette V, Jeanneret R, Le Saux T, Jullien L. Fluorescence to measure light intensity. Nat Methods 2023; 20:1930-1938. [PMID: 37996751 PMCID: PMC10703675 DOI: 10.1038/s41592-023-02063-y] [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: 03/06/2023] [Accepted: 10/02/2023] [Indexed: 11/25/2023]
Abstract
Despite the need for quantitative measurements of light intensity across many scientific disciplines, existing technologies for measuring light dose at the sample of a fluorescence microscope cannot simultaneously retrieve light intensity along with spatial distribution over a wide range of wavelengths and intensities. To address this limitation, we developed two rapid and straightforward protocols that use organic dyes and fluorescent proteins as actinometers. The first protocol relies on molecular systems whose fluorescence intensity decays and/or rises in a monoexponential fashion when constant light is applied. The second protocol relies on a broad-absorbing photochemically inert fluorophore to back-calculate the light intensity from one wavelength to another. As a demonstration of their use, the protocols are applied to quantitatively characterize the spatial distribution of light of various fluorescence imaging systems, and to calibrate illumination of commercially available instruments and light sources.
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Affiliation(s)
- Aliénor Lahlou
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France.
- Sony Computer Science Laboratories, Paris, France.
| | - Hessam Sepasi Tehrani
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Ian Coghill
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Yuriy Shpinov
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Mrinal Mandal
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Isabelle Aujard
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Yuxi Niu
- Institute of Bio- and Geosciences/Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Ladislav Nedbal
- Institute of Bio- and Geosciences/Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Dusan Lazár
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, Palaiseau, France
| | - Willy Supatto
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, Palaiseau, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, Palaiseau, France
| | - Isabelle Eisenmann
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Nicolas Desprat
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Vincent Croquette
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Raphaël Jeanneret
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Thomas Le Saux
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France.
| | - Ludovic Jullien
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France.
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41
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Salafranca J, Ko JK, Mukherjee AK, Fritzsche M, van Grinsven E, Udalova IA. Neutrophil nucleus: shaping the past and the future. J Leukoc Biol 2023; 114:585-594. [PMID: 37480361 PMCID: PMC10673716 DOI: 10.1093/jleuko/qiad084] [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: 03/21/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023] Open
Abstract
Neutrophils are innate immune cells that are key to protecting the host against infection and maintaining body homeostasis. However, if dysregulated, they can contribute to disease, such as in cancer or chronic autoinflammatory disorders. Recent studies have highlighted the heterogeneity in the neutrophil compartment and identified the presence of immature neutrophils and their precursors in these pathologies. Therefore, understanding neutrophil maturity and the mechanisms through which they contribute to disease is critical. Neutrophils were first characterized morphologically by Ehrlich in 1879 using microscopy, and since then, different technologies have been used to assess neutrophil maturity. The advances in the imaging field, including state-of-the-art microscopy and machine learning algorithms for image analysis, reinforce the use of neutrophil nuclear morphology as a fundamental marker of maturity, applicable for objective classification in clinical diagnostics. New emerging approaches, such as the capture of changes in chromatin topology, will provide mechanistic links between the nuclear shape, chromatin organization, and transcriptional regulation during neutrophil maturation.
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Affiliation(s)
- Julia Salafranca
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jacky Ka Ko
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Ananda K Mukherjee
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Marco Fritzsche
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Erinke van Grinsven
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Irina A Udalova
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
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42
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Kuběnová L, Haberland J, Dvořák P, Šamaj J, Ovečka M. Spatiotemporal distribution of reactive oxygen species production, delivery, and use in Arabidopsis root hairs. PLANT PHYSIOLOGY 2023; 193:2337-2360. [PMID: 37666000 PMCID: PMC10663114 DOI: 10.1093/plphys/kiad484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023]
Abstract
Fluorescent selective probes for reactive oxygen species (ROS) detection in living cells are versatile tools for the documentation of ROS production in plant developmental or stress reactions. We employed high-resolution live-cell imaging and semiquantitative analysis of Arabidopsis (Arabidopsis thaliana) stained with CM-H2DCFDA, CellROX Deep Red, and Amplex Red for functional characterization of the spatiotemporal mode of ROS production, delivery, and utilization during root hair formation. Cell viability marker fluorescein diacetate served as a positive control for dye loading and undisturbed root hair tip growth after staining. Using a colocalization analysis with subcellular molecular markers and two root hair mutants with similar phenotypes of nonelongating root hairs, but with contrasting reasons for this impairment, we found that: (i) CM-H2DCFDA is a sensitive probe for ROS generation in the cytoplasm, (ii) CellROX Deep Red labels ROS in mitochondria, (iii) Amplex Red labels apoplastic ROS and mitochondria and shows high selectivity to root hairs, (iv) the root hair defective 2-1 (rhd2-1) mutant with nonfunctional NADPH oxidase RESPIRATORY BURST OXIDASE HOMOLOG PROTEIN C/ROOT HAIR-DEFECTIVE 2 (AtRBOHC/RHD2) has a low level of CM-H2DCFDA-reactive ROS in cytoplasm and lacks Amplex Red-reactive ROS in apoplast, and (v) the ACTIN2-deficient deformed root hairs1-3 (der1-3) mutant is not altered in these aspects. The sensitivity of CellROX Deep Red was documented by discrimination between larger ROS-containing mitochondria and small, yet ROS-free premature mitochondria in the growing tip of root hairs. We characterized spatial changes in ROS production and compartmentalization induced by external ROS modulators, ethylene precursor 1-aminocyclopropane-1-carboxylic acid, and ionophore valinomycin. This dynamic and high-resolution study of ROS production and utilization opens opportunities for precise speciation of particular ROS involved in root hair formation.
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Affiliation(s)
- Lenka Kuběnová
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jan Haberland
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Petr Dvořák
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Miroslav Ovečka
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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43
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Wang H, Han G, Tang H, Zhang R, Liu Z, Sun Y, Liu B, Geng J, Zhang Z. Synchronous Photoactivation-Imaging Fluorophores Break Limitations of Photobleaching and Phototoxicity in Live-cell Microscopy. Anal Chem 2023; 95:16243-16250. [PMID: 37890170 DOI: 10.1021/acs.analchem.3c03064] [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: 10/29/2023]
Abstract
Fluorescence microscopy is one of the most important tools in the studies of cell biology and many other fields, but two fundamental issues, photobleaching and phototoxicity, associated with the fluorophores have still limited its use for long-term and strong-illumination imaging of live cells. Here, we report a new concept of fluorophore engineering chemistry, synchronous photoactivation-imaging (SPI) fluorophores, activating and exciting fluorophores by a single light source to thus avoid the repeated switches between activation and excitation lights. The chemically reconstructed, nonemissive fluorophores can be photolyzed to allow continuous replenishing of "bright-state" probes detectable by standard fluorescent microscopes in the imaging process so as to bypass the photobleaching barrier to greatly extend the imaging period. Equally importantly, SPI fluorophores substantially reduce photocytotoxicity due to the scavenging of reactive oxygen species (ROS) by a photoactivable group and the slow release of "bright-state" probes to minimize ROS generation. Using SPI fluorophores, the time-lapsed confocal (>16 h) and super-resolution (>3 h) imaging of subcellular organelles under intensive illumination (50 MW/cm2) were achieved in live cells.
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Affiliation(s)
- Hong Wang
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Guangmei Han
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Hesen Tang
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Ruilong Zhang
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Zhengjie Liu
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Yingqiang Sun
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Bianhua Liu
- Institute of Solid-State Physics, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| | - Junlong Geng
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Zhongping Zhang
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
- Institute of Solid-State Physics, Chinese Academy of Sciences, Hefei 230031, Anhui, China
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44
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Harada T, Hata S, Takagi R, Komori T, Fukuyama M, Chinen T, Kitagawa D. An antioxidant screen identifies ascorbic acid for prevention of light-induced mitotic prolongation in live cell imaging. Commun Biol 2023; 6:1107. [PMID: 37914777 PMCID: PMC10620154 DOI: 10.1038/s42003-023-05479-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/18/2023] [Indexed: 11/03/2023] Open
Abstract
Phototoxicity is an important issue in fluorescence live imaging of light-sensitive cellular processes such as mitosis. Among several approaches to reduce phototoxicity, the addition of antioxidants to the media has been used as a simple method. Here, we analyzed the impact of phototoxicity on the mitotic progression in fluorescence live imaging of human cells and performed a screen to identify the most efficient antioxidative agents that reduce it. Quantitative analysis shows that high amounts of light illumination cause various mitotic defects such as prolonged mitosis and delays of chromosome alignment and centrosome separation. Among several antioxidants, our screen reveals that ascorbic acid significantly alleviates these phototoxic effects in mitosis. Furthermore, we demonstrate that adding ascorbic acid to the media enables fluorescence imaging of mitotic events at very high temporal resolution without obvious photodamage. Thus, this study provides an optimal method to effectively reduce the phototoxic effects in fluorescence live cell imaging.
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Affiliation(s)
- Tomoki Harada
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shoji Hata
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO) Program, Japan Science and Technology Agency, Honcho Kawaguchi, Saitama, Japan.
| | - Rioka Takagi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takuma Komori
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Masamitsu Fukuyama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takumi Chinen
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Daiju Kitagawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan.
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Park J, Bai B, Ryu D, Liu T, Lee C, Luo Y, Lee MJ, Huang L, Shin J, Zhang Y, Ryu D, Li Y, Kim G, Min HS, Ozcan A, Park Y. Artificial intelligence-enabled quantitative phase imaging methods for life sciences. Nat Methods 2023; 20:1645-1660. [PMID: 37872244 DOI: 10.1038/s41592-023-02041-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 09/11/2023] [Indexed: 10/25/2023]
Abstract
Quantitative phase imaging, integrated with artificial intelligence, allows for the rapid and label-free investigation of the physiology and pathology of biological systems. This review presents the principles of various two-dimensional and three-dimensional label-free phase imaging techniques that exploit refractive index as an intrinsic optical imaging contrast. In particular, we discuss artificial intelligence-based analysis methodologies for biomedical studies including image enhancement, segmentation of cellular or subcellular structures, classification of types of biological samples and image translation to furnish subcellular and histochemical information from label-free phase images. We also discuss the advantages and challenges of artificial intelligence-enabled quantitative phase imaging analyses, summarize recent notable applications in the life sciences, and cover the potential of this field for basic and industrial research in the life sciences.
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Affiliation(s)
- Juyeon Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
| | - Bijie Bai
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - DongHun Ryu
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tairan Liu
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chungha Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
| | - Yi Luo
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mahn Jae Lee
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Luzhe Huang
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeongwon Shin
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Yijie Zhang
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Yuzhu Li
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Geon Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
| | | | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA.
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA, USA.
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea.
- Tomocube, Daejeon, Republic of Korea.
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46
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Balasubramanian H, Hobson CM, Chew TL, Aaron JS. Imagining the future of optical microscopy: everything, everywhere, all at once. Commun Biol 2023; 6:1096. [PMID: 37898673 PMCID: PMC10613274 DOI: 10.1038/s42003-023-05468-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
The optical microscope has revolutionized biology since at least the 17th Century. Since then, it has progressed from a largely observational tool to a powerful bioanalytical platform. However, realizing its full potential to study live specimens is hindered by a daunting array of technical challenges. Here, we delve into the current state of live imaging to explore the barriers that must be overcome and the possibilities that lie ahead. We venture to envision a future where we can visualize and study everything, everywhere, all at once - from the intricate inner workings of a single cell to the dynamic interplay across entire organisms, and a world where scientists could access the necessary microscopy technologies anywhere.
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Affiliation(s)
| | - Chad M Hobson
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Jesse S Aaron
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA.
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47
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561579. [PMID: 37873348 PMCID: PMC10592717 DOI: 10.1101/2023.10.09.561579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
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 three-dimensional 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. We hypothesize 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 auto-fluorescence (hyper-fluorescence) from a homogeneous tissue model (chicken breast), we provide strong evidence supporting this hypothesis. Our 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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48
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Mao W, Bui HTD, Cho W, Yoo HS. Spectroscopic techniques for monitoring stem cell and organoid proliferation in 3D environments for therapeutic development. Adv Drug Deliv Rev 2023; 201:115074. [PMID: 37619771 DOI: 10.1016/j.addr.2023.115074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/22/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Spectroscopic techniques for monitoring stem cell and organoid proliferation have gained significant attention in therapeutic development. Spectroscopic techniques such as fluorescence, Raman spectroscopy, and infrared spectroscopy offer noninvasive and real-time monitoring of biochemical and biophysical changes that occur during stem cell and organoid proliferation. These techniques provide valuable insight into the underlying mechanisms of action of potential therapeutic agents, allowing for improved drug discovery and screening. This review highlights the importance of spectroscopic monitoring of stem cell and organoid proliferation and its potential impact on therapeutic development. Furthermore, this review discusses recent advances in spectroscopic techniques and their applications in stem cell and organoid research. Overall, this review emphasizes the importance of spectroscopic techniques as valuable tools for studying stem cell and organoid proliferation and their potential to revolutionize therapeutic development in the future.
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Affiliation(s)
- Wei Mao
- Department of Biomedical Materials Engineering, Kangwon National University, Chuncheon 24341, Republic of Korea; Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hoai-Thuong Duc Bui
- Department of Biomedical Materials Engineering, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Wanho Cho
- Department of Biomedical Materials Engineering, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hyuk Sang Yoo
- Department of Biomedical Materials Engineering, Kangwon National University, Chuncheon 24341, Republic of Korea; Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea; Institue of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea; Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Republic of Korea.
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49
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Timonen VA, Kerkelä E, Impola U, Penna L, Partanen J, Kilpivaara O, Arvas M, Pitkänen E. DeepIFC: Virtual fluorescent labeling of blood cells in imaging flow cytometry data with deep learning. Cytometry A 2023; 103:807-817. [PMID: 37276178 DOI: 10.1002/cyto.a.24770] [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: 09/30/2022] [Revised: 05/16/2023] [Accepted: 06/02/2023] [Indexed: 06/07/2023]
Abstract
Imaging flow cytometry (IFC) combines flow cytometry with microscopy, allowing rapid characterization of cellular and molecular properties via high-throughput single-cell fluorescent imaging. However, fluorescent labeling is costly and time-consuming. We present a computational method called DeepIFC based on the Inception U-Net neural network architecture, able to generate fluorescent marker images and learn morphological features from IFC brightfield and darkfield images. Furthermore, the DeepIFC workflow identifies cell types from the generated fluorescent images and visualizes the single-cell features generated in a 2D space. We demonstrate that rarer cell types are predicted well when a balanced data set is used to train the model, and the model is able to recognize red blood cells not seen during model training as a distinct entity. In summary, DeepIFC allows accurate cell reconstruction, typing and recognition of unseen cell types from brightfield and darkfield images via virtual fluorescent labeling.
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Affiliation(s)
- Veera A Timonen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Erja Kerkelä
- Advanced Cell Therapy Centre, Finnish Red Cross Blood Service, Vantaa, Finland
| | - Ulla Impola
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Leena Penna
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Jukka Partanen
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- HUSLAB Laboratory of Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Mikko Arvas
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Esa Pitkänen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
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50
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Monfort T, Azzollini S, Brogard J, Clémençon M, Slembrouck-Brec A, Forster V, Picaud S, Goureau O, Reichman S, Thouvenin O, Grieve K. Dynamic full-field optical coherence tomography module adapted to commercial microscopes allows longitudinal in vitro cell culture study. Commun Biol 2023; 6:992. [PMID: 37770552 PMCID: PMC10539404 DOI: 10.1038/s42003-023-05378-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
Dynamic full-field optical coherence tomography (D-FFOCT) has recently emerged as a label-free imaging tool, capable of resolving cell types and organelles within 3D live samples, whilst monitoring their activity at tens of milliseconds resolution. Here, a D-FFOCT module design is presented which can be coupled to a commercial microscope with a stage top incubator, allowing non-invasive label-free longitudinal imaging over periods of minutes to weeks on the same sample. Long term volumetric imaging on human induced pluripotent stem cell-derived retinal organoids is demonstrated, highlighting tissue and cell organization processes such as rosette formation and mitosis as well as cell shape and motility. Imaging on retinal explants highlights single 3D cone and rod structures. An optimal workflow for data acquisition, postprocessing and saving is demonstrated, resulting in a time gain factor of 10 compared to prior state of the art. Finally, a method to increase D-FFOCT signal-to-noise ratio is demonstrated, allowing rapid organoid screening.
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Affiliation(s)
- Tual Monfort
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
- CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, 28 rue de Charenton, F-75012, Paris, France
- Paris Eye Imaging Group, Quinze-Vingts National Eye Hospital, INSERM-DGOS, CIC 1423, 28 rue de Charenton, Paris, 75012, France
| | - Salvatore Azzollini
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Jérémy Brogard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Marilou Clémençon
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Amélie Slembrouck-Brec
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Valerie Forster
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Serge Picaud
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Olivier Goureau
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Sacha Reichman
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Olivier Thouvenin
- Institut Langevin, ESPCI Paris, Université PSL, CNRS, 75005, Paris, France
| | - Kate Grieve
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France.
- CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, 28 rue de Charenton, F-75012, Paris, France.
- Paris Eye Imaging Group, Quinze-Vingts National Eye Hospital, INSERM-DGOS, CIC 1423, 28 rue de Charenton, Paris, 75012, France.
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