1
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Kalyviotis K, Pantazis P. Primed conversion: The emerging player of precise and nontoxic photoconversion. J Microsc 2024; 296:154-161. [PMID: 37937409 DOI: 10.1111/jmi.13244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/17/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
In 2015, we reported primed conversion, a novel way to convert green-to-red photoconvertible fluorescent proteins, which emerges as a powerful tool for precision optical imaging. Primed conversion uses the intercept of blue and red-to-far-red light instead of traditional violet or near-UV light illumination which offers a series of advantages. Here, we review the fundamental principles and applications of primed conversion with a focus on its use in single-cell labelling and lineage tracing. We provide a historical perspective of lineage tracing techniques, thereby covering basic principles of fluorescence, photoconvertible fluorescent proteins, and eventually primed conversion. We then present the molecular requirements for primed conversion to take place and showcase how it can be used for dual-colour high-fidelity lineage tracing. Further, we discuss potential future developments of the primed conversion imaging toolkit that can benefit the study of both development and disease progression.
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2
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Lange M, Granados A, VijayKumar S, Bragantini J, Ancheta S, Kim YJ, Santhosh S, Borja M, Kobayashi H, McGeever E, Solak AC, Yang B, Zhao X, Liu Y, Detweiler AM, Paul S, Theodoro I, Mekonen H, Charlton C, Lao T, Banks R, Xiao S, Jacobo A, Balla K, Awayan K, D'Souza S, Haase R, Dizeux A, Pourquie O, Gómez-Sjöberg R, Huber G, Serra M, Neff N, Pisco AO, Royer LA. A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors. Cell 2024:S0092-8674(24)01147-4. [PMID: 39454574 DOI: 10.1016/j.cell.2024.09.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 05/02/2024] [Accepted: 09/27/2024] [Indexed: 10/28/2024]
Abstract
Elucidating organismal developmental processes requires a comprehensive understanding of cellular lineages in the spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, a dynamic atlas of zebrafish embryonic development that integrates single-cell sequencing time course data with lineage reconstructions facilitated by light-sheet microscopy. This atlas offers high-resolution and in-depth molecular insights into zebrafish development, achieved through the sequencing of individual embryos across ten developmental stages, complemented by reconstructions of cellular trajectories. Zebrahub also incorporates an interactive tool to navigate the complex cellular flows and lineages derived from light-sheet microscopy data, enabling in silico fate-mapping experiments. To demonstrate the versatility of our multimodal resource, we utilize Zebrahub to provide fresh insights into the pluripotency of neuro-mesodermal progenitors (NMPs) and the origins of a joint kidney-hemangioblast progenitor population.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Bin Yang
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Xiang Zhao
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Yang Liu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Sheryl Paul
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | | | - Tiger Lao
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Sheng Xiao
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Keir Balla
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Kyle Awayan
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Robert Haase
- Cluster of Excellence "Physics of Life," TU Dresden, Dresden, Germany
| | - Alexandre Dizeux
- Institute of Physics for Medicine Paris, ESPCI Paris-PSL, Paris, France
| | | | | | - Greg Huber
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mattia Serra
- University of California, San Diego, San Diego, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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3
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Zhang Y, Wang M, Zhu Q, Guo Y, Liu B, Li J, Yao X, Kong C, Zhang Y, Huang Y, Qi H, Wu J, Guo ZV, Dai Q. Long-term mesoscale imaging of 3D intercellular dynamics across a mammalian organ. Cell 2024; 187:6104-6122.e25. [PMID: 39276776 DOI: 10.1016/j.cell.2024.08.026] [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: 01/05/2024] [Revised: 06/06/2024] [Accepted: 08/13/2024] [Indexed: 09/17/2024]
Abstract
A comprehensive understanding of physio-pathological processes necessitates non-invasive intravital three-dimensional (3D) imaging over varying spatial and temporal scales. However, huge data throughput, optical heterogeneity, surface irregularity, and phototoxicity pose great challenges, leading to an inevitable trade-off between volume size, resolution, speed, sample health, and system complexity. Here, we introduce a compact real-time, ultra-large-scale, high-resolution 3D mesoscope (RUSH3D), achieving uniform resolutions of 2.6 × 2.6 × 6 μm3 across a volume of 8,000 × 6,000 × 400 μm3 at 20 Hz with low phototoxicity. Through the integration of multiple computational imaging techniques, RUSH3D facilitates a 13-fold improvement in data throughput and an orders-of-magnitude reduction in system size and cost. With these advantages, we observed premovement neural activity and cross-day visual representational drift across the mouse cortex, the formation and progression of multiple germinal centers in mouse inguinal lymph nodes, and heterogeneous immune responses following traumatic brain injury-all at single-cell resolution, opening up a horizon for intravital mesoscale study of large-scale intercellular interactions at the organ level.
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Affiliation(s)
- Yuanlong Zhang
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Mingrui Wang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518071, China
| | - Qiyu Zhu
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yuduo Guo
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518071, China
| | - Bo Liu
- School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Laboratory of Dynamic Immunobiology, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Jiamin Li
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiao Yao
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Chui Kong
- School of Information Science and Technology, Fudan University, Shanghai 200433, China
| | - Yi Zhang
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Yuchao Huang
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hai Qi
- School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Laboratory of Dynamic Immunobiology, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
| | - Zengcai V Guo
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
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4
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Kumar P, Mondal PP. Multicolor iLIFE (m-iLIFE) volume cytometry for high-throughput imaging of multiple organelles. Sci Rep 2024; 14:23798. [PMID: 39394224 PMCID: PMC11470118 DOI: 10.1038/s41598-024-73667-3] [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: 02/14/2024] [Accepted: 09/19/2024] [Indexed: 10/13/2024] Open
Abstract
To be able to resolve multiple organelles at high throughput is an incredible achievement. This will have immediate implications in a range of fields ranging from fundamental cell biology to translational medicine. To realize such a high-throughput multicolor interrogation modality, we have developed a light-sheet based flow imaging system that is capable of visualizing multiple sub-cellular components with organelle-level resolution. This is possible due to the unique optical design that combines an illumination system comprising two collinear light sheets illuminating the flowing cells and a dedicated dual-color 4f-detection, enabling simultaneous recording of multiple organelles. The system PSF sections up to 4 parallel microfluidic channels through which cells are flowing, and multicolor images of cell cross-sections are recorded. The data is then computationally processed (filtered using ML algorithm, shift-corrected, and merged) and combined to reconstruct the 3D multicolor volume. System testing is conducted using multicolor fluorescent nano-beads (size ∼ 175 nm) and flow-based imaging parameters (PSF size, motion-blur, flow rate, frame rate, and number of cell-sections) are determined for quality imaging. Drug treatment studies were carried out for healthy and cancerous HeLa cells to check the performance of the proposed system. The cells were treated with a drug (Vincristine, which is known to promote mitochondrial fission in cells), and the same is compared with untreated control cells. The proposed multicolor iLIFE system could screen ∼ 800 cells/min (at a flow speed of 2490 μ m/s), and the drug treatment studies were carried out up to 24 h. Studies showed the disintegration of mitochondrial network and dysfunctional lysosomes and their accumulation at the cell membrane, which is a clear indication of cell apoptosis. Compared to control cells (untreated), the mortality is highest at a concentration of 500 nM post 12 h of drug treatment. With the capability of multiorganelle interrogation and organelle-level resolution, the multicolor iLIFE cytometry system is suitably placed to assist optical imaging and biomedical research.
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Affiliation(s)
- Prashant Kumar
- Mondal Lab, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Partha Pratim Mondal
- Mondal Lab, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India.
- Centre for Cryogenic Technology, Indian Institute of Science, Bangalore, 560012, India.
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5
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Hockenberry MA, Daugird TA, Legant WR. Cell dynamics revealed by microscopy advances. Curr Opin Cell Biol 2024; 90:102418. [PMID: 39159598 PMCID: PMC11392612 DOI: 10.1016/j.ceb.2024.102418] [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: 05/01/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/21/2024]
Abstract
Cell biology emerges from spatiotemporally coordinated molecular processes. Recent advances in live-cell microscopy, fueled by a surge in optical, molecular, and computational technologies, have enabled dynamic observations from single molecules to whole organisms. Despite technological leaps, there is still an untapped opportunity to fully leverage their capabilities toward biological insight. We highlight how single-molecule imaging has transformed our understanding of biological processes, with a focus on chromatin organization and transcription in the nucleus. We describe how this was enabled by the close integration of new imaging techniques with analysis tools and discuss the challenges to make a comparable impact at larger scales from organelles to organisms. By highlighting recent successful examples, we describe an outlook of ever-increasing data and the need for seamless integration between dataset visualization and quantification to realize the full potential warranted by advances in new imaging technologies.
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Affiliation(s)
- Max A Hockenberry
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, Chapel Hill, NC, USA
| | - Timothy A Daugird
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wesley R Legant
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Joint Department of Biomedical Engineering, North Carolina State University, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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6
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Pesce L, Ricci P, Sportelli G, Belcari N, Sancataldo G. Expansion and Light-Sheet Microscopy for Nanoscale 3D Imaging. SMALL METHODS 2024; 8:e2301715. [PMID: 38461540 DOI: 10.1002/smtd.202301715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/10/2024] [Indexed: 03/12/2024]
Abstract
Expansion Microscopy (ExM) and Light-Sheet Fluorescence Microscopy (LSFM) are forefront imaging techniques that enable high-resolution visualization of biological specimens. ExM enhances nanoscale investigation using conventional fluorescence microscopes, while LSFM offers rapid, minimally invasive imaging over large volumes. This review explores the joint advancements of ExM and LSFM, focusing on the excellent performance of the integrated modality obtained from the combination of the two, which is refer to as ExLSFM. In doing so, the chemical processes required for ExM, the tailored optical setup of LSFM for examining expanded samples, and the adjustments in sample preparation for accurate data collection are emphasized. It is delve into various specimen types studied using this integrated method and assess its potential for future applications. The goal of this literature review is to enrich the comprehension of ExM and LSFM, encouraging their wider use and ongoing development, looking forward to the upcoming challenges, and anticipating innovations in these imaging techniques.
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Affiliation(s)
- Luca Pesce
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Pietro Ricci
- Department of Applied Physics, University of Barcelona, C/Martí i Franquès, 1, Barcelona, 08028, Spain
| | - Giancarlo Sportelli
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Nicola Belcari
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Giuseppe Sancataldo
- Department of Physics - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, Palermo, 90128, Italy
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7
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Schlomann BH, Pai TW, Sandhu J, Imbert GF, Graham TG, Garcia HG. Spatial microenvironments tune immune response dynamics in the Drosophila larval fat body. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.12.612587. [PMID: 39345471 PMCID: PMC11429692 DOI: 10.1101/2024.09.12.612587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Immune responses in tissues display intricate patterns of gene expression that vary across space and time. While such patterns have been increasingly linked to disease outcomes, the mechanisms that generate them and the logic behind them remain poorly understood. As a tractable model of spatial immune responses, we investigated heterogeneous expression of antimicrobial peptides in the larval fly fat body, an organ functionally analogous to the liver. To capture the dynamics of immune response across the full tissue at single-cell resolution, we established live light sheet fluorescence microscopy of whole larvae. We discovered that expression of antimicrobial peptides occurs in a reproducible spatial pattern, with enhanced expression in the anterior and posterior lobes of the fat body. This pattern correlates with microbial localization via blood flow but is not caused by it: loss of heartbeat suppresses microbial transport but leaves the expression pattern unchanged. This result suggests that regions of the tissue most likely to encounter microbes via blood flow are primed to produce antimicrobials. Spatial transcriptomics revealed that these immune microenvironments are defined by genes spanning multiple biological processes, including lipid-binding proteins that regulate host cell death by the immune system. In sum, the larval fly fat body exhibits spatial compartmentalization of immune activity that resembles the strategic positioning of immune cells in mammals, such as in the liver, gut, and lymph nodes. This finding suggests that tissues may share a conserved spatial organization that optimizes immune responses for antimicrobial efficacy while preventing excessive self-damage.
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Affiliation(s)
- Brandon H. Schlomann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
| | - Ting-Wei Pai
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jazmin Sandhu
- Department of Physics, University of California, Berkeley, CA, USA
| | - Genesis Ferrer Imbert
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
| | - Thomas G.W. Graham
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Hernan G. Garcia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
- Graduate Program in Bioengineering, University of California, Berkeley, CA, USA
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8
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Weiss KR, Huisken J, Khanjani N, Bakalov V, Engle ML, Krzyzanowski MC, Madden T, Maiese DR, Waterfield JR, Williams DN, Wood L, Wu X, Hamilton CM, Huggins W. T-CLEARE: a pilot community-driven tissue clearing protocol repository. Front Bioeng Biotechnol 2024; 12:1304622. [PMID: 39351064 PMCID: PMC11439823 DOI: 10.3389/fbioe.2024.1304622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/18/2024] [Indexed: 10/04/2024] Open
Abstract
Selecting and implementing a tissue clearing protocol is challenging. Established more than 100 years ago, tissue clearing is still a rapidly evolving field of research. There are currently many published protocols to choose from, and each performs better or worse across a range of key evaluation factors (e.g., speed, cost, tissue stability, fluorescence quenching). Additionally, tissue clearing protocols are often optimized for specific experimental contexts, and applying an existing protocol to a new problem can require a lengthy period of adaptation by trial and error. Although the primary literature and review articles provide a useful starting point for optimization, there is growing recognition that results can vary dramatically with changes to tissue type or antibody used. To help address this issue, we have developed a novel, freely available repository of tissue clearing protocols named T-CLEARE (Tissue CLEAring protocol REpository; https://doryworkspace.org/doryviz). T-CLEARE incorporates community responses to an open survey designed to capture details not commonly found in the scientific literature, including modifications to published protocols required for specific use cases and instances when tissue clearing protocols did not perform well (negative results). The goal of T-CLEARE is to help the community share evaluations and modifications of tissue clearing protocols for various tissue types and potentially identify best-in-class methods for a given application.
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Affiliation(s)
- Kurt R. Weiss
- Morgridge Institute for Research, Madison, WI, United States
| | - Jan Huisken
- Morgridge Institute for Research, Madison, WI, United States
| | - Neda Khanjani
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine of University of Southern California, Los Angeles, CA, United States
| | - Vesselina Bakalov
- Bioinformatics and Computational Biology Program, RTI International, Durham, NC, United States
| | - Michelle L. Engle
- Bioinformatics and Computational Biology Program, RTI International, Durham, NC, United States
| | | | - Tom Madden
- Bioinformatics and Computational Biology Program, RTI International, Durham, NC, United States
| | - Deborah R. Maiese
- Bioinformatics and Computational Biology Program, RTI International, Durham, NC, United States
| | - Justin R. Waterfield
- Bioinformatics and Computational Biology Program, RTI International, Durham, NC, United States
| | - David N. Williams
- Bioinformatics and Computational Biology Program, RTI International, Durham, NC, United States
| | - Lauren Wood
- Bioinformatics and Computational Biology Program, RTI International, Durham, NC, United States
| | - Xin Wu
- Bioinformatics and Computational Biology Program, RTI International, Durham, NC, United States
| | - Carol M. Hamilton
- Bioinformatics and Computational Biology Program, RTI International, Durham, NC, United States
| | - Wayne Huggins
- Bioinformatics and Computational Biology Program, RTI International, Durham, NC, United States
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9
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Kramer SN, Antarasen J, Reinholt CR, Kisley L. A practical guide to light-sheet microscopy for nanoscale imaging: Looking beyond the cell. JOURNAL OF APPLIED PHYSICS 2024; 136:091101. [PMID: 39247785 PMCID: PMC11380115 DOI: 10.1063/5.0218262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024]
Abstract
We present a comprehensive guide to light-sheet microscopy (LSM) to assist scientists in navigating the practical implementation of this microscopy technique. Emphasizing the applicability of LSM to image both static microscale and nanoscale features, as well as diffusion dynamics, we present the fundamental concepts of microscopy, progressing through beam profile considerations, to image reconstruction. We outline key practical decisions in constructing a home-built system and provide insight into the alignment and calibration processes. We briefly discuss the conditions necessary for constructing a continuous 3D image and introduce our home-built code for data analysis. By providing this guide, we aim to alleviate the challenges associated with designing and constructing LSM systems and offer scientists new to LSM a valuable resource in navigating this complex field.
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Affiliation(s)
- Stephanie N Kramer
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
| | - Jeanpun Antarasen
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
| | - Cole R Reinholt
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
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10
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Shih CP, Tang WC, Chen P, Chen BC. Applications of Lightsheet Fluorescence Microscopy by High Numerical Aperture Detection Lens. J Phys Chem B 2024; 128:8273-8289. [PMID: 39177503 PMCID: PMC11382282 DOI: 10.1021/acs.jpcb.4c01721] [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: 08/24/2024]
Abstract
This Review explores the evolution, improvements, and recent applications of Light Sheet Fluorescence Microscopy (LSFM) in biological research using a high numerical aperture detection objective (lens) for imaging subcellular structures. The Review begins with an overview of the development of LSFM, tracing its evolution from its inception to its current state and emphasizing key milestones and technological advancements over the years. Subsequently, we will discuss various improvements of LSFM techniques, covering advancements in hardware such as illumination strategies, optical designs, and sample preparation methods that have enhanced imaging capabilities and resolution. The advancements in data acquisition and processing are also included, which provides a brief overview of the recent development of artificial intelligence. Fluorescence probes that were commonly used in LSFM will be highlighted, together with some insights regarding the selection of potential probe candidates for future LSFM development. Furthermore, we also discuss recent advances in the application of LSFM with a focus on high numerical aperture detection objectives for various biological studies. For sample preparation techniques, there are discussions regarding fluorescence probe selection, tissue clearing protocols, and some insights into expansion microscopy. Integrated setups such as adaptive optics, single objective modification, and microfluidics will also be some of the key discussion points in this Review. We hope that this comprehensive Review will provide a holistic perspective on the historical development, technical enhancements, and cutting-edge applications of LSFM, showcasing its pivotal role and future potential in advancing biological research.
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Affiliation(s)
- Chun-Pei Shih
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106319, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei 11529, Taiwan
| | - Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Peilin Chen
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
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11
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Chow DJX, Schartner EP, Corsetti S, Upadhya A, Morizet J, Gunn-Moore FJ, Dunning KR, Dholakia K. Quantifying DNA damage following light sheet and confocal imaging of the mammalian embryo. Sci Rep 2024; 14:20760. [PMID: 39237572 PMCID: PMC11377761 DOI: 10.1038/s41598-024-71443-x] [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: 12/22/2023] [Accepted: 08/28/2024] [Indexed: 09/07/2024] Open
Abstract
Embryo quality assessment by optical imaging is increasing in popularity. Among available optical techniques, light sheet microscopy has emerged as a superior alternative to confocal microscopy due to its geometry, enabling faster image acquisition with reduced photodamage to the sample. However, previous assessments of photodamage induced by imaging may have failed to measure more subtle impacts. In this study, we employed DNA damage as a sensitive indicator of photodamage. We use light sheet microscopy with excitation at a wavelength of 405 nm for imaging embryo autofluorescence and compare its performance to laser scanning confocal microscopy. At an equivalent signal-to-noise ratio for images acquired with both modalities, light sheet microscopy reduced image acquisition time by ten-fold, and did not induce DNA damage when compared to non-imaged embryos. In contrast, imaging with confocal microscopy led to significantly higher levels of DNA damage within embryos and had a higher photobleaching rate. Light sheet imaging is also capable of inducing DNA damage within the embryo but requires multiple cycles of volumetric imaging. Collectively, this study confirms that light sheet microscopy is faster and safer than confocal microscopy for imaging live embryos, indicating its potential as a label-free diagnostic for embryo quality.
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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
| | - Erik P Schartner
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
| | - Stella Corsetti
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, UK.
| | - Avinash Upadhya
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
- Centre of Light for Life, The University of Adelaide, Adelaide, Australia
| | - Josephine Morizet
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | - Frank J Gunn-Moore
- School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | - 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
| | - Kishan Dholakia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia.
- Centre of Light for Life, The University of Adelaide, Adelaide, Australia.
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, UK.
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12
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Fukushima HS, Ikeda T, Ikeda S, Takeda H. Cell cycle length governs heterochromatin reprogramming during early development in non-mammalian vertebrates. EMBO Rep 2024; 25:3300-3323. [PMID: 38943003 PMCID: PMC11315934 DOI: 10.1038/s44319-024-00188-5] [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: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/30/2024] Open
Abstract
Heterochromatin marks such as H3K9me3 undergo global erasure and re-establishment after fertilization, and the proper reprogramming of H3K9me3 is essential for early development. Despite the widely conserved dynamics of heterochromatin reprogramming in invertebrates and non-mammalian vertebrates, previous studies have shown that the underlying mechanisms may differ between species. Here, we investigate the molecular mechanism of H3K9me3 dynamics in medaka (Japanese killifish, Oryzias latipes) as a non-mammalian vertebrate model, and show that rapid cell cycle during cleavage stages causes DNA replication-dependent passive erasure of H3K9me3. We also find that cell cycle slowing, toward the mid-blastula transition, permits increasing nuclear accumulation of H3K9me3 histone methyltransferase Setdb1, leading to the onset of H3K9me3 re-accumulation. We further demonstrate that cell cycle length in early development also governs H3K9me3 reprogramming in zebrafish and Xenopus laevis. Together with the previous studies in invertebrates, we propose that a cell cycle length-dependent mechanism for both global erasure and re-accumulation of H3K9me3 is conserved among rapid-cleavage species of non-mammalian vertebrates and invertebrates such as Drosophila, C. elegans, Xenopus and teleost fish.
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Affiliation(s)
- Hiroto S Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
- Center for Integrative Medical Sciences, RIKEN, Yokohama, 230-0045, Japan.
| | - Takafumi Ikeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, 603-8555, Japan
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Shinra Ikeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan.
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13
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Heiles B, Nelissen F, Terwiel D, Park BM, Munoz Ibarra E, Matalliotakis A, Waasdorp R, Ara T, Barturen-Larrea P, Duan M, Shapiro MG, Gazzola V, Maresca D. Nonlinear sound-sheet microscopy: imaging opaque organs at the capillary and cellular scale. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.605825. [PMID: 39211282 PMCID: PMC11361007 DOI: 10.1101/2024.07.31.605825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Light-sheet fluorescence microscopy has revolutionized biology by visualizing dynamic cellular processes in three dimensions. However, light scattering in thick tissue and photobleaching of fluorescent reporters limit this method to studying thin or translucent specimens. Here we show that non-diffractive ultrasonic beams used in conjunction with a cross-amplitude modulation sequence and nonlinear acoustic reporters enable fast and volumetric imaging of targeted biological functions. We report volumetric imaging of tumor gene expression at the cm 3 scale using genetically encoded gas vesicles, and localization microscopy of currently uncharted cerebral capillary networks using intravascular microbubble contrast agents. Nonlinear sound-sheet microscopy provides a ∼64x acceleration in imaging speed, ∼35x increase in imaged volume and ∼4x increase in classical imaging resolution compared to the state-of-the-art in biomolecular ultrasound.
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14
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Liberali P, Schier AF. The evolution of developmental biology through conceptual and technological revolutions. Cell 2024; 187:3461-3495. [PMID: 38906136 DOI: 10.1016/j.cell.2024.05.053] [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: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Developmental biology-the study of the processes by which cells, tissues, and organisms develop and change over time-has entered a new golden age. After the molecular genetics revolution in the 80s and 90s and the diversification of the field in the early 21st century, we have entered a phase when powerful technologies provide new approaches and open unexplored avenues. Progress in the field has been accelerated by advances in genomics, imaging, engineering, and computational biology and by emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary technologies have led to remarkable progress in understanding animal development. We describe how classic questions in gene regulation, pattern formation, morphogenesis, organogenesis, and stem cell biology are being revisited. We discuss the connections of development with evolution, self-organization, metabolism, time, and ecology. We speculate how developmental biology might evolve in an era of synthetic biology, artificial intelligence, and human engineering.
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Affiliation(s)
- Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland.
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15
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Serrano Nájera G, Plum AM, Steventon B, Weijer CJ, Serra M. Control of Modular Tissue Flows Shaping the Embryo in Avian Gastrulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.04.601785. [PMID: 39026830 PMCID: PMC11257462 DOI: 10.1101/2024.07.04.601785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Avian gastrulation requires coordinated flows of thousands of cells to form the body plan. We quantified these flows using their fundamental kinematic units: one attractor and two repellers constituting its Dynamic Morphoskeleton (DM). We have also elucidated the mechanistic origin of the attractor, marking the primitive streak (PS), and controlled its shape, inducing gastrulation flows in the chick embryo that are typical of other vertebrates. However, the origins of repellers and dynamic embryo shape remain unclear. Here, we address these questions using active matter physics and experiments. Repeller 1, separating the embryo proper (EP) from extraembryonic (EE) tissues, arises from the tug-of-war between EE epiboly and EP isotropic myosin-induced active stress. Repeller 2, bisecting the anterior and posterior PS and associated with embryo shape change, arises from anisotropic myosin-induced active intercalation in the mesendoderm. Combining mechanical confinement with inhibition of mesendoderm induction, we eliminated either one or both repellers, as predicted by our model. Our results reveal a remarkable modularity of avian gastrulation flows delineated by the DM, uncovering the mechanistic roles of EE epiboly, EP active constriction, mesendoderm intercalation and ingression. These findings offer a new perspective for deconstructing morphogenetic flows, uncovering their modular origin, and aiding synthetic morphogenesis.
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Affiliation(s)
| | - Alex M. Plum
- Department of Physics, University of California San Diego, CA 92093, USA
| | - Ben Steventon
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Cornelis J. Weijer
- Division of Molec. Cell and Dev. Biology, School of Life Sciences, Univ. of Dundee, UK
| | - Mattia Serra
- Department of Physics, University of California San Diego, CA 92093, USA
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16
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Feng R, Xie J, Gao L. EDTP enhances and protects the fluorescent signal of GFP in cleared and expanded tissues. Sci Rep 2024; 14:15279. [PMID: 38961181 PMCID: PMC11222453 DOI: 10.1038/s41598-024-66398-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: 02/08/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
Advanced 3D high-resolution imaging techniques are essential for investigating biological challenges, such as neural circuit analysis and tumor microenvironment in intact tissues. However, the fluorescence signal emitted by endogenous fluorescent proteins in cleared or expanded biological samples gradually diminishes with repeated irradiation and prolonged imaging, compromising its ability to accurately depict the underlying scientific problem. We have developed a strategy to preserve fluorescence in cleared and expanded tissue samples during prolonged high-resolution three-dimensional imaging. We evaluated various compounds at different concentrations to determine their ability to enhance fluorescence intensity and resistance to photobleaching while maintaining the structural integrity of the tissue. Specifically, we investigated the impact of EDTP utilization on GFP, as it has been observed to significantly improve fluorescence intensity, resistance to photobleaching, and maintain fluorescence during extended room temperature storage. This breakthrough will facilitate extended hydrophilic and hydrogel-based clearing and expansion methods for achieving long-term high-resolution 3D imaging of cleared biological tissues by effectively safeguarding fluorescent proteins within the tissue.
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Affiliation(s)
- Ruili Feng
- Fudan University, Shanghai, 200433, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China.
| | - Jiongfang Xie
- Fudan University, Shanghai, 200433, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
| | - Liang Gao
- Fudan University, Shanghai, 200433, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
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17
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Ertürk A. Deep 3D histology powered by tissue clearing, omics and AI. Nat Methods 2024; 21:1153-1165. [PMID: 38997593 DOI: 10.1038/s41592-024-02327-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/28/2024] [Indexed: 07/14/2024]
Abstract
To comprehensively understand tissue and organism physiology and pathophysiology, it is essential to create complete three-dimensional (3D) cellular maps. These maps require structural data, such as the 3D configuration and positioning of tissues and cells, and molecular data on the constitution of each cell, spanning from the DNA sequence to protein expression. While single-cell transcriptomics is illuminating the cellular and molecular diversity across species and tissues, the 3D spatial context of these molecular data is often overlooked. Here, I discuss emerging 3D tissue histology techniques that add the missing third spatial dimension to biomedical research. Through innovations in tissue-clearing chemistry, labeling and volumetric imaging that enhance 3D reconstructions and their synergy with molecular techniques, these technologies will provide detailed blueprints of entire organs or organisms at the cellular level. Machine learning, especially deep learning, will be essential for extracting meaningful insights from the vast data. Further development of integrated structural, molecular and computational methods will unlock the full potential of next-generation 3D histology.
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Affiliation(s)
- Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Zentrum München, Neuherberg, Germany.
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University, Munich, Germany.
- School of Medicine, Koç University, İstanbul, Turkey.
- Deep Piction GmbH, Munich, Germany.
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18
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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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19
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Otomo K, Omura T, Nozawa Y, Edwards SJ, Sato Y, Saito Y, Yagishita S, Uchida H, Watakabe Y, Naitou K, Yanai R, Sahara N, Takagi S, Katayama R, Iwata Y, Shiokawa T, Hayakawa Y, Otsuka K, Watanabe-Takano H, Haneda Y, Fukuhara S, Fujiwara M, Nii T, Meno C, Takeshita N, Yashiro K, Rosales Rocabado JM, Kaku M, Yamada T, Oishi Y, Koike H, Cheng Y, Sekine K, Koga JI, Sugiyama K, Kimura K, Karube F, Kim H, Manabe I, Nemoto T, Tainaka K, Hamada A, Brismar H, Susaki EA. descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques. Nat Commun 2024; 15:4941. [PMID: 38866781 PMCID: PMC11169475 DOI: 10.1038/s41467-024-49131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktop-equipped SPIM for cleared specimens), a low-cost ($20,000-50,000), low-expertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a three-dimensional manner. Academically open-sourced ( https://github.com/dbsb-juntendo/descSPIM ), descSPIM allows routine three-dimensional imaging of cleared samples in minutes. Thus, the dissemination of descSPIM will accelerate biomedical discoveries driven by tissue clearing technologies.
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Affiliation(s)
- Kohei Otomo
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Takaki Omura
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Neurosurgery, University of Tokyo, Tokyo, Japan
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Nozawa
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
| | - Steven J Edwards
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yukihiko Sato
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuri Saito
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shigehiro Yagishita
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hitoshi Uchida
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yuki Watakabe
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kiyotada Naitou
- Department of Basic Veterinary Science, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Rin Yanai
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Naruhiko Sahara
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Satoshi Takagi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yusuke Iwata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiro Shiokawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kensuke Otsuka
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry, Chiba, Japan
| | - Haruko Watanabe-Takano
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Yuka Haneda
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Miku Fujiwara
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takenobu Nii
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Chikara Meno
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoki Takeshita
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kenta Yashiro
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Juan Marcelo Rosales Rocabado
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaru Kaku
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tatsuya Yamada
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Yumiko Oishi
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Koike
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yinglan Cheng
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keisuke Sekine
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, Tokyo, Japan
| | - Jun-Ichiro Koga
- The Second Department of Internal Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Kaori Sugiyama
- Institute for Advanced Research of Biosystem Dynamics, Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Kenichi Kimura
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Fuyuki Karube
- Lab of Histology and Cytology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hyeree Kim
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Manabe
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomomi Nemoto
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akinobu Hamada
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Etsuo A Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan.
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan.
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan.
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20
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Katoh TA, Fukai YT, Ishibashi T. Optical microscopic imaging, manipulation, and analysis methods for morphogenesis research. Microscopy (Oxf) 2024; 73:226-242. [PMID: 38102756 PMCID: PMC11154147 DOI: 10.1093/jmicro/dfad059] [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: 06/30/2023] [Revised: 11/20/2023] [Accepted: 03/22/2024] [Indexed: 12/17/2023] Open
Abstract
Morphogenesis is a developmental process of organisms being shaped through complex and cooperative cellular movements. To understand the interplay between genetic programs and the resulting multicellular morphogenesis, it is essential to characterize the morphologies and dynamics at the single-cell level and to understand how physical forces serve as both signaling components and driving forces of tissue deformations. In recent years, advances in microscopy techniques have led to improvements in imaging speed, resolution and depth. Concurrently, the development of various software packages has supported large-scale, analyses of challenging images at the single-cell resolution. While these tools have enhanced our ability to examine dynamics of cells and mechanical processes during morphogenesis, their effective integration requires specialized expertise. With this background, this review provides a practical overview of those techniques. First, we introduce microscopic techniques for multicellular imaging and image analysis software tools with a focus on cell segmentation and tracking. Second, we provide an overview of cutting-edge techniques for mechanical manipulation of cells and tissues. Finally, we introduce recent findings on morphogenetic mechanisms and mechanosensations that have been achieved by effectively combining microscopy, image analysis tools and mechanical manipulation techniques.
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Affiliation(s)
- Takanobu A Katoh
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yohsuke T Fukai
- Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Tomoki Ishibashi
- Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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21
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Liang S, Fu K, Li X, Wang Z. Unveiling the spatiotemporal dynamics of membrane fouling: A focused review on dynamic fouling characterization techniques and future perspectives. Adv Colloid Interface Sci 2024; 328:103179. [PMID: 38754212 DOI: 10.1016/j.cis.2024.103179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 03/12/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
Membrane technology has emerged as a crucial method for obtaining clean water from unconventional sources in the face of water scarcity. It finds wide applications in wastewater treatment, advanced treatment, and desalination of seawater and brackish water. However, membrane fouling poses a huge challenge that limits the development of membrane-based water treatment technologies. Characterizing the dynamics of membrane fouling is crucial for understanding its development, mechanisms, and effective mitigation. Instrumental techniques that enable in situ or real-time characterization of the dynamics of membrane fouling provide insights into the temporal and spatial evolution of fouling, which play a crucial role in understanding the fouling mechanism and the formulation of membrane control strategies. This review consolidates existing knowledge about the principal advanced instrumental analysis technologies employed to characterize the dynamics of membrane fouling, in terms of membrane structure, morphology, and intermolecular forces. Working principles, applications, and limitations of each technique are discussed, enabling researchers to select appropriate methods for their specific studies. Furthermore, prospects for the future development of dynamic characterization techniques for membrane fouling are discussed, underscoring the need for continued research and innovation in this field to overcome the challenges posed by membrane fouling.
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Affiliation(s)
- Shuling Liang
- School of Environmental Science and Engineering, Shanghai Institute of Pollution Control and Ecological Security, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Kunkun Fu
- School of Aerospace Engineering and Applied Mechanics, Tongji University, Shanghai 200092, China
| | - Xuesong Li
- School of Environmental Science and Engineering, Shanghai Institute of Pollution Control and Ecological Security, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China.
| | - Zhiwei Wang
- School of Environmental Science and Engineering, Shanghai Institute of Pollution Control and Ecological Security, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
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22
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Lu Z, Zuo S, Shi M, Fan J, Xie J, Xiao G, Yu L, Wu J, Dai Q. Long-term intravital subcellular imaging with confocal scanning light-field microscopy. Nat Biotechnol 2024:10.1038/s41587-024-02249-5. [PMID: 38802562 DOI: 10.1038/s41587-024-02249-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 04/17/2024] [Indexed: 05/29/2024]
Abstract
Long-term observation of subcellular dynamics in living organisms is limited by background fluorescence originating from tissue scattering or dense labeling. Existing confocal approaches face an inevitable tradeoff among parallelization, resolution and phototoxicity. Here we present confocal scanning light-field microscopy (csLFM), which integrates axially elongated line-confocal illumination with the rolling shutter in scanning light-field microscopy (sLFM). csLFM enables high-fidelity, high-speed, three-dimensional (3D) imaging at near-diffraction-limit resolution with both optical sectioning and low phototoxicity. By simultaneous 3D excitation and detection, the excitation intensity can be reduced below 1 mW mm-2, with 15-fold higher signal-to-background ratio over sLFM. We imaged subcellular dynamics over 25,000 timeframes in optically challenging environments in different species, such as migrasome delivery in mouse spleen, retractosome generation in mouse liver and 3D voltage imaging in Drosophila. Moreover, csLFM facilitates high-fidelity, large-scale neural recording with reduced crosstalk, leading to high orientation selectivity to visual stimuli, similar to two-photon microscopy, which aids understanding of neural coding mechanisms.
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Affiliation(s)
- Zhi Lu
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- Zhejiang Hehu Technology, Hangzhou, China
- Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou, China
| | - Siqing Zuo
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Minghui Shi
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiaqi Fan
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jingyu Xie
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Guihua Xiao
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
- Shanghai AI Laboratory, Shanghai, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
- Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China.
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23
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Bentahar S, Gómez-Gaviro MV, Desco M, Ripoll J, Fernández R. Multispectral imaging for characterizing autofluorescent tissues. Sci Rep 2024; 14:12084. [PMID: 38802477 PMCID: PMC11130125 DOI: 10.1038/s41598-024-61020-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Selective Plane Illumination Microscopy (SPIM) has become an emerging technology since its first application for 3D in-vivo imaging of the development of a living organism. An extensive number of works have been published, improving both the speed of acquisition and the resolution of the systems. Furthermore, multispectral imaging allows the effective separation of overlapping signals associated with different fluorophores from the spectrum over the whole field-of-view of the analyzed sample. To eliminate the need of using fluorescent dyes, this technique can also be applied to autofluorescence imaging. However, the effective separation of the overlapped spectra in autofluorescence imaging necessitates the use of mathematical tools. In this work, we explore the application of a method based on Principal Component Analysis (PCA) that enables tissue characterization upon spectral autofluorescence data without the use of fluorophores. Thus, enabling the separation of different tissue types in fixed and living samples with no need of staining techniques. Two procedures are described for acquiring spectral data, including a single excitation based method and a multi-excitation scanning approach. In both cases, we demonstrate the effective separation of various tissue types based on their unique autofluorescence spectra.
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Affiliation(s)
- Sara Bentahar
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain
| | | | - Manuel Desco
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Jorge Ripoll
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
| | - Roberto Fernández
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain.
- Departamento de Física, Ingeniería de Sistemas y Teoría de la Señal, Universidad de Alicante, Alicante, Spain.
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24
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Tomizawa Y, Wali KH, Surti M, Suhail Y, Kshitiz, Hoshino K. Lightsheet microscopy integrates single-cell optical visco-elastography and fluorescence cytometry of 3D live tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.20.590392. [PMID: 38766194 PMCID: PMC11100606 DOI: 10.1101/2024.04.20.590392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Most common cytometry methods, including flow cytometry, observe suspended or fixed cells and cannot evaluate their structural roles in 3D tissues. However, cellular physical interactions are critical in physiological, developmental, and pathological processes. Here, we present a novel optical visco-elastography that characterizes single-cellular physical interactions by applying in-situ micro-mechanical perturbation to live microtissues under 3D lightsheet microscopy. The 4D digital image correlation (DIC) analysis of ~20,000 nodes tracked the compressive deformation of 3D tissues containing ~500 cells. The computational 3D image segmentation allowed cell-by-cell qualitative observation and statistical analysis, directly correlating multi-channel fluorescence and viscoelasticity. To represent epithelia-stroma interactions, we used a 3D organoid model of maternal-fetal interface and visualized solid-like, well-aligned displacement and liquid-like random motion between individual cells. The statistical analysis through our unique cytometry confirmed that endometrial stromal fibroblasts stiffen in response to decidualization. Moreover, we demonstrated in the 3D model that interaction with placental extravillous trophoblasts partially reverses the attained stiffness, which was supported by the gene expression analysis. Placentation shares critical cellular and molecular significance with various fundamental biological events such as cancer metastasis, wound healing, and gastrulation. Our analysis confirmed existing beliefs and discovered new insights, proving the broad applicability of our method.
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Affiliation(s)
- Yuji Tomizawa
- Department of Biomedical Engineering, University of Connecticut, CT
| | - Khadija H Wali
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, CT
| | - Manav Surti
- Department of Biomedical Engineering, University of Connecticut, CT
| | - Yasir Suhail
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, CT
| | - Kshitiz
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, CT
- Systems Biology Institute, Yale University, West Haven, CT
| | - Kazunori Hoshino
- Department of Biomedical Engineering, University of Connecticut, CT
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25
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Mandal M, Scerbo P, Coghill I, Riou JF, Bochet CG, Ducos B, Bensimon D, Le Saux T, Aujard I, Jullien L. Caged Dexamethasone to Photo-control the Development of Embryos through Activation of the Glucocorticoid Receptor. Chemistry 2024; 30:e202400579. [PMID: 38350020 DOI: 10.1002/chem.202400579] [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: 02/12/2024] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 02/15/2024]
Abstract
Efficient tools for controlling molecular functions with exquisite spatiotemporal resolution are much in demand to investigate biological processes in living systems. Here we report an easily synthesized caged dexamethasone for photo-activating cytoplasmic proteins fused to the glucocorticoid receptor. In the dark, it is stable in vitro as well as in vivo in both zebrafish (Danio rerio) and Xenopus sp, two significant models of vertebrates. In contrast, it liberates dexamethasone upon UV illumination, which has been harnessed to interfere with developmental steps in embryos of these animals. Interestingly, this new system is biologically orthogonal to the one for photo-activating proteins fused to the estrogen ERT receptor, which brings great prospect for activating two distinct proteins down to the single cell level.
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Affiliation(s)
- Mrinal Mandal
- PASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Pierluigi Scerbo
- Laboratoire de Physique de l'Ecole Normale Supérieure, Paris Sciences Lettres University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005, Paris, France
| | - Ian Coghill
- PASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Jean-François Riou
- Laboratory of Developmental Biology, Institute of Biology Paris-Seine, Sorbonne University, CNRS, 9, Quai Saint-Bernard, 75252, Paris, Cedex 05, France
| | - Christian G Bochet
- Department of Chemistry, University of Fribourg, 9 Ch. du Musée, CH-1700, Fribourg, Switzerland
| | - Bertrand Ducos
- Laboratoire de Physique de l'Ecole Normale Supérieure, Paris Sciences Lettres University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005, Paris, France
- High Throughput qPCR Core Facility, Ecole Normale Supérieure, Paris Sciences Lettres University, 46 Rue d'Ulm, 75005, Paris, France
| | - David Bensimon
- Laboratoire de Physique de l'Ecole Normale Supérieure, Paris Sciences Lettres University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005, Paris, France
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Thomas Le Saux
- PASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Isabelle Aujard
- PASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
| | - Ludovic Jullien
- PASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24, rue Lhomond, 75005, Paris, France
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26
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Kairišs K, Sokolova N, Zilova L, Schlagheck C, Reinhardt R, Baumbach T, Faragó T, van de Kamp T, Wittbrodt J, Weinhardt V. Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach. Sci Rep 2024; 14:8543. [PMID: 38609416 PMCID: PMC11015006 DOI: 10.1038/s41598-024-58766-5] [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: 01/08/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The development of an organism is orchestrated by the spatial and temporal expression of genes. Accurate visualisation of gene expression patterns in the context of the surrounding tissues offers a glimpse into the mechanisms that drive morphogenesis. We developed correlative light-sheet fluorescence microscopy and X-ray computed tomography approach to map gene expression patterns to the whole organism`s 3D anatomy. We show that this multimodal approach is applicable to gene expression visualized by protein-specific antibodies and fluorescence RNA in situ hybridisation offering a detailed understanding of individual phenotypic variations in model organisms. Furthermore, the approach offers a unique possibility to identify tissues together with their 3D cellular and molecular composition in anatomically less-defined in vitro models, such as organoids. We anticipate that the visual and quantitative insights into the 3D distribution of gene expression within tissue architecture, by multimodal approach developed here, will be equally valuable for reference atlases of model organisms development, as well as for comprehensive screens, and morphogenesis studies of in vitro models.
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Affiliation(s)
- Kristaps Kairišs
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Lucie Zilova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
| | - Christina Schlagheck
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Robert Reinhardt
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tomáš Faragó
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Thomas van de Kamp
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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27
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Wang J, Xu X, Ye H, Zhang X, Shi G. Interferometric modulation for generating extended light sheet: improving field of view. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:046501. [PMID: 38629030 PMCID: PMC11020319 DOI: 10.1117/1.jbo.29.4.046501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
Significance Light-sheet fluorescence microscopy (LSFM) has emerged as a powerful and versatile imaging technique renowned for its remarkable features, including high-speed 3D tomography, minimal photobleaching, and low phototoxicity. The interference light-sheet fluorescence microscope, with its larger field of view (FOV) and more uniform axial resolution, possesses significant potential for a wide range of applications in biology and medicine. Aim The aim of this study is to investigate the interference behavior among multiple light sheets (LSs) in LSFM and optimize the FOV and resolution of the light-sheet fluorescence microscope. Approach We conducted a detailed investigation of the interference effects among LSs through theoretical derivation and numerical simulations, aiming to find optimal parameters. Subsequently, we constructed a customized system of multi-LSFM that incorporates both interference light sheets (ILS) and noninterference light-sheet configurations. We performed beam imaging and microsphere imaging tests to evaluate the FOV and axial resolution of these systems. Results Using our custom-designed light-sheet fluorescence microscope, we captured the intensity distribution profiles of both interference and noninterference light sheets (NILS). Additionally, we conducted imaging tests on microspheres to assess their imaging outcomes. The ILS not only exhibits a larger FOV compared to the NILS but also demonstrates a more uniform axial resolution. Conclusions By effectively modulating the interference among multiple LSs, it is possible to optimize the intensity distribution of the LSs, expand the FOV, and achieve a more uniform axial resolution.
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Affiliation(s)
- Jixiang Wang
- University of Science and Technology of China, School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, Hefei, China
- Chinese Academy of Science, Suzhou Institute of Biomedical Engineering and Technology, Jiangsu Key Laboratory of Medical Optics, Suzhou, China
| | - Xin Xu
- University of Science and Technology of China, School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, Hefei, China
- Chinese Academy of Science, Suzhou Institute of Biomedical Engineering and Technology, Jiangsu Key Laboratory of Medical Optics, Suzhou, China
| | - Hong Ye
- Chinese Academy of Science, Suzhou Institute of Biomedical Engineering and Technology, Jiangsu Key Laboratory of Medical Optics, Suzhou, China
| | - Xin Zhang
- Chinese Academy of Science, Suzhou Institute of Biomedical Engineering and Technology, Jiangsu Key Laboratory of Medical Optics, Suzhou, China
| | - Guohua Shi
- University of Science and Technology of China, School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, Hefei, China
- Chinese Academy of Science, Suzhou Institute of Biomedical Engineering and Technology, Jiangsu Key Laboratory of Medical Optics, Suzhou, China
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28
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Luu P, Fraser SE, Schneider F. More than double the fun with two-photon excitation microscopy. Commun Biol 2024; 7:364. [PMID: 38531976 DOI: 10.1038/s42003-024-06057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
For generations researchers have been observing the dynamic processes of life through the lens of a microscope. This has offered tremendous insights into biological phenomena that span multiple orders of time- and length-scales ranging from the pure magic of molecular reorganization at the membrane of immune cells, to cell migration and differentiation during development or wound healing. Standard fluorescence microscopy techniques offer glimpses at such processes in vitro, however, when applied in intact systems, they are challenged by reduced signal strengths and signal-to-noise ratios that result from deeper imaging. As a remedy, two-photon excitation (TPE) microscopy takes a special place, because it allows us to investigate processes in vivo, in their natural environment, even in a living animal. Here, we review the fundamental principles underlying TPE aimed at basic and advanced microscopy users interested in adopting TPE for intravital imaging. We focus on applications in neurobiology, present current trends towards faster, wider and deeper imaging, discuss the combination with photon counting technologies for metabolic imaging and spectroscopy, as well as highlight outstanding issues and drawbacks in development and application of these methodologies.
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Affiliation(s)
- Peter Luu
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Scott E Fraser
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
- Alfred Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Falk Schneider
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA.
- Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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29
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Schindler-Johnson M, Petridou NI. Collective effects of cell cleavage dynamics. Front Cell Dev Biol 2024; 12:1358971. [PMID: 38559810 PMCID: PMC10978805 DOI: 10.3389/fcell.2024.1358971] [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: 12/20/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
A conserved process of early embryonic development in metazoans is the reductive cell divisions following oocyte fertilization, termed cell cleavages. Cell cleavage cycles usually start synchronously, lengthen differentially between the embryonic cells becoming asynchronous, and cease before major morphogenetic events, such as germ layer formation and gastrulation. Despite exhibiting species-specific characteristics, the regulation of cell cleavage dynamics comes down to common controllers acting mostly at the single cell/nucleus level, such as nucleus-to-cytoplasmic ratio and zygotic genome activation. Remarkably, recent work has linked cell cleavage dynamics to the emergence of collective behavior during embryogenesis, including pattern formation and changes in embryo-scale mechanics, raising the question how single-cell controllers coordinate embryo-scale processes. In this review, we summarize studies across species where an association between cell cleavages and collective behavior was made, discuss the underlying mechanisms, and propose that cell-to-cell variability in cell cleavage dynamics can serve as a mechanism of long-range coordination in developing embryos.
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Affiliation(s)
- Magdalena Schindler-Johnson
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Nicoletta I. Petridou
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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30
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Yin J, Liang R, Hou H, Miao Y, Yu L. Light sheet fluorescence microscopy with active optical manipulation. OPTICS LETTERS 2024; 49:1193-1196. [PMID: 38426971 DOI: 10.1364/ol.515280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024]
Abstract
We present a light sheet fluorescence microscopy (LSFM) with active optical manipulation by using linear optical tweezers (LOTs). In this method, two coaxially transmitting laser beams of different wavelengths are shaped using cylindrical lenses to form a linear optical trapping perpendicular to the optical axis and an excitation light sheet (LS) parallel to the optical axis, respectively. Multiple large-sized polystyrene fluorescent microspheres are stably captured by LOTs, and their rotation angles around specific rotation axes are precisely controlled. During a sample rotation, the stationary excitation LS scans the sample to obtain fluorescence sectioning images of the sample at different angles.
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31
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Hafa L, Breideband L, Ramirez Posada L, Torras N, Martinez E, Stelzer EHK, Pampaloni F. Light Sheet-Based Laser Patterning Bioprinting Produces Long-Term Viable Full-Thickness Skin Constructs. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2306258. [PMID: 37822216 DOI: 10.1002/adma.202306258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/04/2023] [Indexed: 10/13/2023]
Abstract
Tissue engineering holds great promise for biomedical research and healthcare, offering alternatives to animal models and enabling tissue regeneration and organ transplantation. 3D bioprinting stands out for its design flexibility and reproducibility. Here, an integrated fluorescent light sheet bioprinting and imaging system is presented that combines high printing speed (0.66 mm3 /s) and resolution (9 µm) with light sheet-based imaging. This approach employs direct laser patterning and a static light sheet for confined voxel crosslinking in photocrosslinkable materials. The developed bioprinter enables real-time monitoring of hydrogel crosslinking using fluorescent recovery after photobleaching (FRAP) and brightfield imaging as well as in situ light sheet imaging of cells. Human fibroblasts encapsulated in a thiol-ene click chemistry-based hydrogel exhibited high viability (83% ± 4.34%) and functionality. Furthermore, full-thickness skin constructs displayed characteristics of both epidermal and dermal layers and remained viable for 41 days. The integrated approach demonstrates the capabilities of light sheet bioprinting, offering high speed, resolution, and real-time characterization. Future enhancements involving solid-state laser scanning devices such as acousto-optic deflectors and modulators will further enhance resolution and speed, opening new opportunities in light-based bioprinting and advancing tissue engineering.
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Affiliation(s)
- Levin Hafa
- Institute of Cell Biology and Neurosciences (IZN), Buchman Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany
| | - Louise Breideband
- Institute of Cell Biology and Neurosciences (IZN), Buchman Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany
| | - Lucas Ramirez Posada
- Institute of Cell Biology and Neurosciences (IZN), Buchman Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany
| | - Núria Torras
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain
| | - Elena Martinez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain
| | - Ernst H K Stelzer
- Institute of Cell Biology and Neurosciences (IZN), Buchman Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany
| | - Francesco Pampaloni
- Institute of Cell Biology and Neurosciences (IZN), Buchman Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany
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32
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Shi Y, Tabet JS, Milkie DE, Daugird TA, Yang CQ, Ritter AT, Giovannucci A, Legant WR. Smart lattice light-sheet microscopy for imaging rare and complex cellular events. Nat Methods 2024; 21:301-310. [PMID: 38167656 PMCID: PMC11216155 DOI: 10.1038/s41592-023-02126-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024]
Abstract
Light-sheet microscopes enable rapid high-resolution imaging of biological specimens; however, biological processes span spatiotemporal scales. Moreover, long-term phenotypes are often instigated by rare or fleeting biological events that are difficult to capture with a single imaging modality. Here, to overcome this limitation, we present smartLLSM, a microscope that incorporates artificial intelligence-based instrument control to autonomously switch between epifluorescent inverted imaging and lattice light-sheet microscopy (LLSM). We apply this approach to two unique processes: cell division and immune synapse formation. In each context, smartLLSM provides population-level statistics across thousands of cells and autonomously captures multicolor three-dimensional datasets or four-dimensional time-lapse movies of rare events at rates that dramatically exceed human capabilities. From this, we quantify the effects of Taxol dose on spindle structure and kinetochore dynamics in dividing cells and of antigen strength on cytotoxic T lymphocyte engagement and lytic granule polarization at the immune synapse. Overall, smartLLSM efficiently detects rare events within heterogeneous cell populations and records these processes with high spatiotemporal four-dimensional imaging over statistically significant replicates.
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Affiliation(s)
- Yu Shi
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jimmy S Tabet
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothy A Daugird
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chelsea Q Yang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Andrea Giovannucci
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Wesley R Legant
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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33
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Das R, Sinha S, Li X, Kirkpatrick TR, Thirumalai D. Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis. eLife 2024; 12:RP87966. [PMID: 38241331 PMCID: PMC10945604 DOI: 10.7554/elife.87966] [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: 01/21/2024] Open
Abstract
A recent experiment on zebrafish blastoderm morphogenesis showed that the viscosity (η) of a non-confluent embryonic tissue grows sharply until a critical cell packing fraction (ϕS). The increase in η up to ϕS is similar to the behavior observed in several glass-forming materials, which suggests that the cell dynamics is sluggish or glass-like. Surprisingly, η is a constant above ϕS. To determine the mechanism of this unusual dependence of η on ϕ, we performed extensive simulations using an agent-based model of a dense non-confluent two-dimensional tissue. We show that polydispersity in the cell size, and the propensity of the cells to deform, results in the saturation of the available free area per cell beyond a critical packing fraction. Saturation in the free space not only explains the viscosity plateau above ϕS but also provides a relationship between equilibrium geometrical packing to the dramatic increase in the relaxation dynamics.
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Affiliation(s)
- Rajsekhar Das
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - Sumit Sinha
- Department of Physics, University of Texas at AustinAustinUnited States
| | - Xin Li
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - TR Kirkpatrick
- Institute for Physical Science and Technology, University of MarylandCollege ParkUnited States
| | - D Thirumalai
- Department of Chemistry, University of Texas at AustinAustinUnited States
- Department of Physics, University of Texas at AustinAustinUnited States
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34
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Rahimpouresfahani F, Tabatabaei N, Rezai P. High-throughput light sheet imaging of adult and larval C. elegans Parkinson's disease model using a low-cost optofluidic device and a fluorescent microscope. RSC Adv 2024; 14:626-639. [PMID: 38173569 PMCID: PMC10759043 DOI: 10.1039/d3ra06323b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Recent advancements at the interface of microfluidics technology and light sheet fluorescence microscopy have opened the door for high-throughput and high-content investigation of C. elegans disease models. In this paper, we report on the development of a simple, miniaturized, and low-cost optofluidic platform that can be added to a conventional inverted fluorescent microscope for continuous light sheet imaging of transgenic worm populations with high lateral and axial resolutions of 1.1 µm and 2.4 µm, respectively. The optofluidic device is made entirely of PDMS with integrated optics for light sheet generation. Laser excitation is delivered to the device via a low-cost free space laser, and cross-sections of worm populations are imaged as they pass continuously through a channel. Results show the platform can image NW1229 whole worms with pan-neural fluorescent expression at a throughput of >20 worms per minute at L3 and young adult (YA) stages. As a benchmark test, we show that the low-cost device can quantify the reduced neuronal expressions of L3 and YA NW1229 worms when exposed to 500 µM 6-OHDA neurodegenerative agent. Following the benchmark validation, we utilized the platform in a novel application for imaging human alpha-synuclein reporter in populations of Parkinson's transgenic model (ERS100). Results show the ability of the low-cost platform to reliably detect and quantify the anomalous neural phenotypic changes in ERS100 populations at L3 and YA stages with high spatial resolution. The findings of this study show the potential of our low-cost optofluidic add-on platform to equip conventional fluorescent microscopes with light sheet capability for quantitative phenotypic studies of transgenic C. elegans at high resolution and throughput.
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Affiliation(s)
- Faraz Rahimpouresfahani
- Department of Mechanical Engineering, York University 4700 Keele St Toronto M3J 1P3 Ontario Canada +1-416-7362100
| | - Nima Tabatabaei
- Department of Mechanical Engineering, York University 4700 Keele St Toronto M3J 1P3 Ontario Canada +1-416-7362100
| | - Pouya Rezai
- Department of Mechanical Engineering, York University 4700 Keele St Toronto M3J 1P3 Ontario Canada +1-416-7362100
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35
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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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36
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Kang YG, Park K, Hyeon MG, Yang TD, Choi Y. Three-dimensional imaging in reflection phase microscopy with minimal axial scanning. OPTICS EXPRESS 2023; 31:44741-44753. [PMID: 38178536 DOI: 10.1364/oe.510519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
Reflection phase microscopy is a valuable tool for acquiring three-dimensional (3D) images of objects due to its capability of optical sectioning. The conventional method of constructing a 3D map is capturing 2D images at each depth with a mechanical scanning finer than the optical sectioning. This not only compromises sample stability but also slows down the acquisition process, imposing limitations on its practical applications. In this study, we utilized a reflection phase microscope to acquire 2D images at depth locations significantly spaced apart, far beyond the range of optical sectioning. By employing a numerical propagation, we successfully filled the information gap between the acquisition layers, and then constructed complete 3D maps of objects with substantially reduced number of axial scans. Our experimental results also demonstrated the effectiveness of this approach in enhancing imaging speed while maintaining the accuracy of the reconstructed 3D structures. This technique has the potential to improve the applicability of reflection phase microscopy in diverse fields such as bioimaging and material science.
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37
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Lee SH, Son HJ. Second Wave, Late-Stage Neuroinflammation in Cleared Brains of Aged 5xFAD Alzheimer's Mice Detected by Macrolaser Light Sheet Microscopy Imaging. Int J Mol Sci 2023; 24:17058. [PMID: 38069392 PMCID: PMC10707588 DOI: 10.3390/ijms242317058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
This study leverages the innovative imaging capabilities of macrolaser light-sheet microscopy to elucidate the 3D spatial visualization of AD-associated neuropathologic networks in the transparent brains of 44-week-old 5xFAD mice. Brain samples from ten AD and seven control mice were prepared through a hydrophilic tissue-clearing pipeline and immunostained with thioflavin S (β-amyloid), anti-CD11b antibody (microglia), and anti-ACSA-2 antibody (astrocytes). The 5xFAD group exhibited significantly higher average total surface volumes of β-amyloid accumulation than the control group (AD, 898,634,368 µm3 [383,355,488-1,324,986,752]; control, 33,320,178 µm3 [11,156,785-65,390,988], p = 0.0006). Within the AD group, there was significant interindividual and interindividual variability concerning the number and surface volume of individual amyloid particles throughout the entire brain. In the context of neuroinflammation, the 5xFAD group showed significantly higher average total surface volumes of anti-ACSA-2-labeled astrocytes (AD, 59,064,360 µm3 [27,815,500-222,619,280]; control, 20,272,722 µm3 [9,317,288-27,223,352], p = 0.0047) and anti-CD11b labeled microglia (AD, 51,210,100 µm3 [15,309,118-135,532,144]; control, 23,461,593 µm3 [14,499,170-27,924,110], p = 0.0162) than the control group. Contrary to the long-standing finding that early-stage neuroinflammation precedes the subsequent later-stage of neurodegeneration, our data reveal that the second wave, late-stage active neuroinflammation persists in the aged AD brains, even as they continue to show signs of ongoing neurodegeneration and significant amyloid accumulation.
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Affiliation(s)
- Suk Hyun Lee
- Department of Radiology, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, Republic of Korea
| | - Hye Joo Son
- Department of Nuclear Medicine, Dankook University Medical Center, Dankook University College of Medicine, Cheonan 31116, Republic of Korea
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38
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Zhang G, Li X, Zhang Y, Han X, Li X, Yu J, Liu B, Wu J, Yu L, Dai Q. Bio-friendly long-term subcellular dynamic recording by self-supervised image enhancement microscopy. Nat Methods 2023; 20:1957-1970. [PMID: 37957429 PMCID: PMC10703694 DOI: 10.1038/s41592-023-02058-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 09/29/2023] [Indexed: 11/15/2023]
Abstract
Fluorescence microscopy has become an indispensable tool for revealing the dynamic regulation of cells and organelles. However, stochastic noise inherently restricts optical interrogation quality and exacerbates observation fidelity when balancing the joint demands of high frame rate, long-term recording and low phototoxicity. Here we propose DeepSeMi, a self-supervised-learning-based denoising framework capable of increasing signal-to-noise ratio by over 12 dB across various conditions. With the introduction of newly designed eccentric blind-spot convolution filters, DeepSeMi effectively denoises images with no loss of spatiotemporal resolution. In combination with confocal microscopy, DeepSeMi allows for recording organelle interactions in four colors at high frame rates across tens of thousands of frames, monitoring migrasomes and retractosomes over a half day, and imaging ultra-phototoxicity-sensitive Dictyostelium cells over thousands of frames. Through comprehensive validations across various samples and instruments, we prove DeepSeMi to be a versatile and biocompatible tool for breaking the shot-noise limit.
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Affiliation(s)
- Guoxun Zhang
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Xiaopeng Li
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanlong Zhang
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Xiaofei Han
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Xinyang Li
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jinqiang Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Boqi Liu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Shanghai AI Laboratory, Shanghai, China.
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
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Jiang T, Gong H, Yuan J. Whole-brain Optical Imaging: A Powerful Tool for Precise Brain Mapping at the Mesoscopic Level. Neurosci Bull 2023; 39:1840-1858. [PMID: 37715920 PMCID: PMC10661546 DOI: 10.1007/s12264-023-01112-y] [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: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 09/18/2023] Open
Abstract
The mammalian brain is a highly complex network that consists of millions to billions of densely-interconnected neurons. Precise dissection of neural circuits at the mesoscopic level can provide important structural information for understanding the brain. Optical approaches can achieve submicron lateral resolution and achieve "optical sectioning" by a variety of means, which has the natural advantage of allowing the observation of neural circuits at the mesoscopic level. Automated whole-brain optical imaging methods based on tissue clearing or histological sectioning surpass the limitation of optical imaging depth in biological tissues and can provide delicate structural information in a large volume of tissues. Combined with various fluorescent labeling techniques, whole-brain optical imaging methods have shown great potential in the brain-wide quantitative profiling of cells, circuits, and blood vessels. In this review, we summarize the principles and implementations of various whole-brain optical imaging methods and provide some concepts regarding their future development.
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Affiliation(s)
- Tao Jiang
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
| | - Hui Gong
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jing Yuan
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
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40
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Van Impe M, Caboor L, Deleeuw V, De Rycke K, Vanhooydonck M, De Backer J, Segers P, Sips P. Application of an automated analysis framework for pulsed-wave Doppler cardiac ultrasound measurements to generate reference data in adult zebrafish. Am J Physiol Regul Integr Comp Physiol 2023; 325:R782-R796. [PMID: 37811715 DOI: 10.1152/ajpregu.00103.2023] [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: 05/16/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
High-frequency cardiac ultrasound is the only well-established method to characterize in vivo cardiovascular function in adult zebrafish noninvasively. Pulsed-wave Doppler imaging allows measurements of blood flow velocities at well-defined anatomical positions, but the measurements and results obtained using this technique need to be analyzed carefully, taking into account the substantial baseline variability within one recording and the possibility for operator bias. To address these issues and to increase throughput by limiting hands-on analysis time, we have developed a fully automated processing pipeline. This framework enables the fast, unbiased analysis of all cardiac cycles in a zebrafish pulsed-wave Doppler recording of both atrioventricular valve flow as well as aortic valve flow without operator-dependent inputs. Applying this automated pipeline to a large number of recordings from wild-type zebrafish shows a strong agreement between the automated results and manual annotations performed by an experienced operator. The reference data obtained from this analysis showed that the early wave peak during ventricular inflow is lower for female compared with male zebrafish. We also found that the peaks of the ventricular inflow and outflow waves as well as the peaks of the regurgitation waves are all correlated positively with body surface area. In general, the presented reference data, as well as the automated Doppler measurement processing tools developed and validated in this study will facilitate future (high-throughput) cardiovascular phenotyping studies in adult zebrafish ultimately leading to a more comprehensive understanding of human (genetic) cardiovascular diseases.
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Affiliation(s)
- Matthias Van Impe
- IBiTech-BioMMedA, Department of Electronics and Information Systems, Ghent University, Ghent, Belgium
| | - Lisa Caboor
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Violette Deleeuw
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Karo De Rycke
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Michiel Vanhooydonck
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Julie De Backer
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Patrick Segers
- IBiTech-BioMMedA, Department of Electronics and Information Systems, Ghent University, Ghent, Belgium
| | - Patrick Sips
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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41
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Natesan G, Hamilton T, Deeds EJ, Shah PK. Novel metrics reveal new structure and unappreciated heterogeneity in Caenorhabditis elegans development. PLoS Comput Biol 2023; 19:e1011733. [PMID: 38113280 PMCID: PMC10763962 DOI: 10.1371/journal.pcbi.1011733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 01/03/2024] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
High throughput experimental approaches are increasingly allowing for the quantitative description of cellular and organismal phenotypes. Distilling these large volumes of complex data into meaningful measures that can drive biological insight remains a central challenge. In the quantitative study of development, for instance, one can resolve phenotypic measures for single cells onto their lineage history, enabling joint consideration of heritable signals and cell fate decisions. Most attempts to analyze this type of data, however, discard much of the information content contained within lineage trees. In this work we introduce a generalized metric, which we term the branch edit distance, that allows us to compare any two embryos based on phenotypic measurements in individual cells. This approach aligns those phenotypic measurements to the underlying lineage tree, providing a flexible and intuitive framework for quantitative comparisons between, for instance, Wild-Type (WT) and mutant developmental programs. We apply this novel metric to data on cell-cycle timing from over 1300 WT and RNAi-treated Caenorhabditis elegans embryos. Our new metric revealed surprising heterogeneity within this data set, including subtle batch effects in WT embryos and dramatic variability in RNAi-induced developmental phenotypes, all of which had been missed in previous analyses. Further investigation of these results suggests a novel, quantitative link between pathways that govern cell fate decisions and pathways that pattern cell cycle timing in the early embryo. Our work demonstrates that the branch edit distance we propose, and similar metrics like it, have the potential to revolutionize our quantitative understanding of organismal phenotype.
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Affiliation(s)
- Gunalan Natesan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
| | - Timothy Hamilton
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
| | - Eric J. Deeds
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
| | - Pavak K. Shah
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
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42
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Chattaraj S, Torre M, Kalcher C, Stukowski A, Morganti S, Reali A, Pasqualini FS. SEM 2: Introducing mechanics in cell and tissue modeling using coarse-grained homogeneous particle dynamics. APL Bioeng 2023; 7:046118. [PMID: 38075209 PMCID: PMC10699888 DOI: 10.1063/5.0166829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/14/2023] [Indexed: 09/03/2024] Open
Abstract
Modeling multiscale mechanics in shape-shifting engineered tissues, such as organoids and organs-on-chip, is both important and challenging. In fact, it is difficult to model relevant tissue-level large non-linear deformations mediated by discrete cell-level behaviors, such as migration and proliferation. One approach to solve this problem is subcellular element modeling (SEM), where ensembles of coarse-grained particles interacting via empirically defined potentials are used to model individual cells while preserving cell rheology. However, an explicit treatment of multiscale mechanics in SEM was missing. Here, we incorporated analyses and visualizations of particle level stress and strain in the open-source software SEM++ to create a new framework that we call subcellular element modeling and mechanics or SEM2. To demonstrate SEM2, we provide a detailed mechanics treatment of classical SEM simulations including single-cell creep, migration, and proliferation. We also introduce an additional force to control nuclear positioning during migration and proliferation. Finally, we show how SEM2 can be used to model proliferation in engineered cell culture platforms such as organoids and organs-on-chip. For every scenario, we present the analysis of cell emergent behaviors as offered by SEM++ and examples of stress or strain distributions that are possible with SEM2. Throughout the study, we only used first-principles literature values or parametric studies, so we left to the Discussion a qualitative comparison of our insights with recently published results. The code for SEM2 is available on GitHub at https://github.com/Synthetic-Physiology-Lab/sem2.
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Affiliation(s)
- Sandipan Chattaraj
- Synthetic Physiology Lab, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy
| | - Michele Torre
- Computational Mechanics and Advanced Materials Group, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy
| | | | | | - Simone Morganti
- Computational Mechanics and Advanced Materials Group, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy
| | - Alessandro Reali
- Computational Mechanics and Advanced Materials Group, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy
| | - Francesco Silvio Pasqualini
- Synthetic Physiology Lab, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy
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43
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Mitchell NP, Cislo DJ. TubULAR: tracking in toto deformations of dynamic tissues via constrained maps. Nat Methods 2023; 20:1980-1988. [PMID: 38057529 PMCID: PMC10848277 DOI: 10.1038/s41592-023-02081-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/10/2023] [Indexed: 12/08/2023]
Abstract
A common motif in biology is the arrangement of cells into tubes, which further transform into complex shapes. Traditionally, analysis of dynamic tissues has relied on inspecting static snapshots, live imaging of cross-sections or tracking isolated cells in three dimensions. However, capturing the interplay between in-plane and out-of-plane behaviors requires following the full surface as it deforms and integrating cell-scale motions into collective, tissue-scale deformations. Here, we present an analysis framework that builds in toto maps of tissue deformations by following tissue parcels in a static material frame of reference. Our approach then relates in-plane and out-of-plane behaviors and decomposes complex deformation maps into elementary contributions. The tube-like surface Lagrangian analysis resource (TubULAR) provides an open-source implementation accessible either as a standalone toolkit or as an extension of the ImSAnE package used in the developmental biology community. We demonstrate our approach by analyzing shape change in the embryonic Drosophila midgut and beating zebrafish heart. The method naturally generalizes to in vitro and synthetic systems and provides ready access to the mechanical mechanisms relating genetic patterning to organ shape change.
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Affiliation(s)
- Noah P Mitchell
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, CA, USA.
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Dillon J Cislo
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA, USA.
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA.
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44
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Guo X, Zhao F, Zhu J, Zhu D, Zhao Y, Fei P. Rapid 3D isotropic imaging of whole organ with double-ring light-sheet microscopy and self-learning side-lobe elimination. BIOMEDICAL OPTICS EXPRESS 2023; 14:6206-6221. [PMID: 38420327 PMCID: PMC10898557 DOI: 10.1364/boe.505217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 03/02/2024]
Abstract
Bessel-like plane illumination forms a new type of light-sheet microscopy with ultra-long optical sectioning distance that enables rapid 3D imaging of fine cellular structures across an entire large tissue. However, the side-lobe excitation of conventional Bessel light sheets severely impairs the quality of the reconstructed 3D image. Here, we propose a self-supervised deep learning (DL) approach that can completely eliminate the residual side lobes for a double-ring-modulated non-diffraction light-sheet microscope, thereby substantially improving the axial resolution of the 3D image. This lightweight DL model utilizes the own point spread function (PSF) of the microscope as prior information without the need for external high-resolution microscopy data. After a quick training process based on a small number of datasets, the grown-up model can restore sidelobe-free 3D images with near isotropic resolution for diverse samples. Using an advanced double-ring light-sheet microscope in conjunction with this efficient restoration approach, we demonstrate 5-minute rapid imaging of an entire mouse brain with a size of ∼12 mm × 8 mm × 6 mm and achieve uniform isotropic resolution of ∼4 µm (1.6-µm voxel) capable of discerning the single neurons and vessels across the whole brain.
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Affiliation(s)
- Xinyi Guo
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fang Zhao
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jingtan Zhu
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Dan Zhu
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, 430074, Wuhan, China
- Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yuxuan Zhao
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Peng Fei
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, 430074, Wuhan, China
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45
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Venkatareddy N, Mandal J, Maiti PK. Effect of confinement and topology: 2-TIPS vs. MIPS. SOFT MATTER 2023; 19:8561-8576. [PMID: 37905347 DOI: 10.1039/d3sm00796k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
2-TIPS (two temperature induced phase separation) refers to the phase separation phenomenon observed in mixtures of active and passive particles which are modelled using scalar activity. The active particles are connected to a thermostat at high temperature while the passive particles are connected to the thermostat at low temperature and the relative temperature difference between "hot" and "cold" particles is taken as the measure of the activity χ of the non-equilibrium system. The study of such binary mixtures of hot and cold particles under various kinds of confinement is an important problem in many physical and biological processes. The nature and extent of phase separation are heavily influenced by the geometry of confinement, activity, and density of the non-equilibrium binary mixture. Investigating such 3D binary mixtures confined by parallel walls, we observe that the active and passive particles phase separate, but the extent of phase separation is reduced compared to bulk phase separation at high densities and enhanced at low densities. However, when the binary mixture of active and passive particles is confined inside a spherical cavity, the phase separation is radial for small radii of the confining sphere and the extent of phase separation is higher compared to their bulk counterparts. Confinement leads to interesting properties in the passive (cold) region like enhanced layering and high compression in the direction parallel to the confining wall. In 2D, both the bulk and confined systems of the binary mixture show a significant decrement in the extent of phase separation at higher densities. This observation is attributed to the trapping of active particles inside the passive cluster, which increases with density. Thus the 2D systems show structures more akin to dense-dilute phase co-existence, which is observed in motility induced phase separation in 2D active systems. The binary mixture constrained on the spherical surface also shows similar phase co-existence. Our analyses reveal that the coexistent densities observed in 2-TIPS on the spherical surface agree with the findings of previous studies on MIPS in active systems on a sphere.
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Affiliation(s)
- Nayana Venkatareddy
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Jaydeep Mandal
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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Barron-Ortiz D, Cadena-Nava RD, Pérez-Parets E, Licea-Rodriguez J, Gualda EJ, Hernandez-Cordero J, Loza-Alvarez P, Rocha-Mendoza I. Volumetric Temperature Mapping Using Light-Sheet Microscopy and Upconversion Fluorescence from Micro- and Nano-Rare Earth Composites. MICROMACHINES 2023; 14:2097. [PMID: 38004954 PMCID: PMC10673603 DOI: 10.3390/mi14112097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
We present a combination of light-sheet excitation and two-dimensional fluorescence intensity ratio (FIR) measurements as a simple and promising technique for three-dimensional temperature mapping. The feasibility of this approach is demonstrated with samples fabricated with sodium yttrium fluoride nanoparticles co-doped with rare-earth ytterbium and erbium ions (NaYF4:Yb3+/Er3+) incorporated into polydimethylsiloxane (PDMS) as a host material. In addition, we also evaluate the technique using lipid-coated NaYF4:Yb3+/Er3+ nanoparticles immersed in agar. The composite materials show upconverted (UC) fluorescence bands when excited by a 980 nm near-infrared laser light-sheet. Using a single CMOS camera and a pair of interferometric optical filters to specifically image the two thermally-coupled bands (at 525 and 550 nm), the two-dimensional FIR and, hence, the temperature map can be readily obtained. The proposed method can take optically sectioned (confocal-like) images with good optical resolution over relatively large samples (up to the millimetric scale) for further 3D temperature reconstruction.
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Affiliation(s)
- Dannareli Barron-Ortiz
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana, No. 3918, Zona Playitas, Ensenada 22860, Mexico;
| | - Ruben D. Cadena-Nava
- Centro de Nanociencias y Nanotecnología (CNyN), Universidad Nacional Autónoma de México (UNAM), Km 107 Carretera Tijuana-Ensenada, Pedregal Playitas, Ensenada 22860, Mexico;
| | - Enric Pérez-Parets
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Spain
| | - Jacob Licea-Rodriguez
- Centro de Investigación en Ingeniería y Ciencias Aplicadas (CIICAp), Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - Emilio J. Gualda
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Spain
- Department of Agri-Food Engineering and Biotechnology (DEAB), Universitat Politècnica de Catalunya, Esteve Terradas 8, 08860 Castelldefels, Spain;
| | - Juan Hernandez-Cordero
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, A.P. 70-360, Mexico City 04510, Mexico;
| | - Pablo Loza-Alvarez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Spain
| | - Israel Rocha-Mendoza
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana, No. 3918, Zona Playitas, Ensenada 22860, Mexico;
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47
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Yang D, Zhang S, Zheng C, Zhou G, Hu Y, Hao Q. Refractive index tomography with a physics-based optical neural network. BIOMEDICAL OPTICS EXPRESS 2023; 14:5886-5903. [PMID: 38021108 PMCID: PMC10659804 DOI: 10.1364/boe.504242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023]
Abstract
The non-interference three-dimensional refractive index (RI) tomography has attracted extensive attention in the life science field for its simple system implementation and robust imaging performance. However, the complexity inherent in the physical propagation process poses significant challenges when the sample under study deviates from the weak scattering approximation. Such conditions complicate the task of achieving global optimization with conventional algorithms, rendering the reconstruction process both time-consuming and potentially ineffective. To address such limitations, this paper proposes an untrained multi-slice neural network (MSNN) with an optical structure, in which each layer has a clear corresponding physical meaning according to the beam propagation model. The network does not require pre-training and performs good generalization and can be recovered through the optimization of a set of intensity images. Concurrently, MSNN can calibrate the intensity of different illumination by learnable parameters, and the multiple backscattering effects have also been taken into consideration by integrating a "scattering attenuation layer" between adjacent "RI" layers in the MSNN. Both simulations and experiments have been conducted carefully to demonstrate the effectiveness and feasibility of the proposed method. Experimental results reveal that MSNN can enhance clarity with increased efficiency in RI tomography. The implementation of MSNN introduces a novel paradigm for RI tomography.
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Affiliation(s)
- Delong Yang
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Shaohui Zhang
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
- Yangtze Delta Region Academy of Beijing Institute of Technology, China
| | - Chuanjian Zheng
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Guocheng Zhou
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Yao Hu
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Qun Hao
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
- Yangtze Delta Region Academy of Beijing Institute of Technology, China
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48
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Dennis EJ, Bibawi P, Dhanerawala ZM, Lynch LA, Wang SSH, Brody CD. Princeton RAtlas: A Common Coordinate Framework for Fully cleared, Whole Rattus norvegicus Brains. Bio Protoc 2023; 13:e4854. [PMID: 37900100 PMCID: PMC10603261 DOI: 10.21769/bioprotoc.4854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 10/31/2023] Open
Abstract
Whole-brain clearing and imaging methods are becoming more common in mice but have yet to become standard in rats, at least partially due to inadequate clearing from most available protocols. Here, we build on recent mouse-tissue clearing and light-sheet imaging methods and develop and adapt them to rats. We first used cleared rat brains to create an open-source, 3D rat atlas at 25 μm resolution. We then registered and imported other existing labeled volumes and made all of the code and data available for the community (https://github.com/emilyjanedennis/PRA) to further enable modern, whole-brain neuroscience in the rat. Key features • This protocol adapts iDISCO (Renier et al., 2014) and uDISCO (Pan et al., 2016) tissue-clearing techniques to consistently clear rat brains. • This protocol also decreases the number of working hours per day to fit in an 8 h workday. Graphical overview.
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Affiliation(s)
- Emily Jane Dennis
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, USA
| | - Peter Bibawi
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Neurology Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zahra M. Dhanerawala
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Laura A. Lynch
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
| | - Samuel S.-H. Wang
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
| | - Carlos D. Brody
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, USA
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49
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Gao C, Zhang T, Wei Y, Liu Q, Ma L, Gao M, Zhao X, Wang Y, Chen D, Sun L, Wang J, Chen J. Development of a Microfluidic Flow Cytometer with a Uniform Optical Field (Uni-μFCM) Enabling Quantitative Analysis of Single-Cell Proteins and Its Applications in Leukemia Gating, Tumor Classification, and Hierarchy of Cancer Stem Cells. ACS Sens 2023; 8:3498-3509. [PMID: 37602731 PMCID: PMC10521140 DOI: 10.1021/acssensors.3c01060] [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: 05/25/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023]
Abstract
Fast and quantitative estimation of single-cell proteins with various distribution patterns remains a technical challenge. Here, a microfluidic flow cytometer with a uniform optical field (Uni-μFCM) was developed, which enabled the translation of multicolor fluorescence signals of bound antibodies into targeted protein numbers with arbitrary distributions of biological cells. As the core of Uni-μFCM, a uniform optical field for optical excitation and fluorescence detection was realized by adopting a microfabricated metal window to shape the optical beam for excitation, which was modeled and validated by both numerical simulation and experimental characterization. After the validation of Uni-μFCM in single-cell protein quantification by measuring single-cell expressions of three transcriptional factors from four cell lines of variable sizes and origins, Uni-μFCM was applied to (1) quantify membrane and cytoplasmic markers of myeloid and lymphocytic leukocytes to classify cell lines and normal and patient blood samples; (2) measure single-cell expressions of key cytokines affiliated with gene stabilities, differentiating paired oral and colon tumor cell lines with varied malignancies, and (3) quantify single-cell stemming markers of liver tumor cell lines, cell subtypes, and liver patient samples to determine a variety of lineage hierarchy. By quantitatively assessing complex cellular phenotypes, Uni-μFCM substantially expanded the phenotypic space accessible to single-cell applications in leukemia gating, tumor classification, and hierarchy determination of cancer stem cells.
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Affiliation(s)
- Chiyuan Gao
- State
Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- School
of Future Technology, University of Chinese
Academy of Sciences, Beijing100049, People’s
Republic of China
| | - Ting Zhang
- State
Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- School
of Future Technology, University of Chinese
Academy of Sciences, Beijing100049, People’s
Republic of China
| | - Yuanchen Wei
- State
Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
| | - Qinghua Liu
- State
Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- School
of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Liangliang Ma
- State
Key Laboratory of Molecular Oncology,National
Cancer Center/National Clinical Research Center for Cancer/Cancer
Hospital Chinese Academy of Medical Sciences and Peking Union Medical
College, Beijing100021, People’s Republic
of China
| | - Mengge Gao
- Peking
University People’s Hospital, Peking University Institute of
Hematology, National Clinical Research Center for Hematologic Disease,
Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing100044, People’s Republic of China
| | - Xiaosu Zhao
- Peking
University People’s Hospital, Peking University Institute of
Hematology, National Clinical Research Center for Hematologic Disease,
Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing100044, People’s Republic of China
| | - Yixiang Wang
- Peking
University
Hospital of Stomatology, Beijing100081, People’s
Republic of China
| | - Deyong Chen
- State
Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- School
of Future Technology, University of Chinese
Academy of Sciences, Beijing100049, People’s
Republic of China
- School
of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Lichao Sun
- State
Key Laboratory of Molecular Oncology,National
Cancer Center/National Clinical Research Center for Cancer/Cancer
Hospital Chinese Academy of Medical Sciences and Peking Union Medical
College, Beijing100021, People’s Republic
of China
| | - Junbo Wang
- State
Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- School
of Future Technology, University of Chinese
Academy of Sciences, Beijing100049, People’s
Republic of China
- School
of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Jian Chen
- State
Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- School
of Future Technology, University of Chinese
Academy of Sciences, Beijing100049, People’s
Republic of China
- School
of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
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50
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Zeng CW, Tsai HJ. The Promising Role of a Zebrafish Model Employed in Neural Regeneration Following a Spinal Cord Injury. Int J Mol Sci 2023; 24:13938. [PMID: 37762240 PMCID: PMC10530783 DOI: 10.3390/ijms241813938] [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: 07/27/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Spinal cord injury (SCI) is a devastating event that results in a wide range of physical impairments and disabilities. Despite the advances in our understanding of the biological response to injured tissue, no effective treatments are available for SCIs at present. Some studies have addressed this issue by exploring the potential of cell transplantation therapy. However, because of the abnormal microenvironment in injured tissue, the survival rate of transplanted cells is often low, thus limiting the efficacy of such treatments. Many studies have attempted to overcome these obstacles using a variety of cell types and animal models. Recent studies have shown the utility of zebrafish as a model of neural regeneration following SCIs, including the proliferation and migration of various cell types and the involvement of various progenitor cells. In this review, we discuss some of the current challenges in SCI research, including the accurate identification of cell types involved in neural regeneration, the adverse microenvironment created by SCIs, attenuated immune responses that inhibit nerve regeneration, and glial scar formation that prevents axonal regeneration. More in-depth studies are needed to fully understand the neural regeneration mechanisms, proteins, and signaling pathways involved in the complex interactions between the SCI microenvironment and transplanted cells in non-mammals, particularly in the zebrafish model, which could, in turn, lead to new therapeutic approaches to treat SCIs in humans and other mammals.
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Affiliation(s)
- Chih-Wei Zeng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Huai-Jen Tsai
- Department of Life Science, Fu Jen Catholic University, New Taipei City 242062, Taiwan
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