1
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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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2
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Anticevic I, Otten C, Vinkovic L, Jukic L, Popovic M. Tyrosyl-DNA phosphodiesterase 1 (TDP1) and SPRTN protease repair histone 3 and topoisomerase 1 DNA-protein crosslinks in vivo. Open Biol 2023; 13:230113. [PMID: 37788708 PMCID: PMC10547559 DOI: 10.1098/rsob.230113] [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: 04/24/2023] [Accepted: 08/14/2023] [Indexed: 10/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are frequent and damaging DNA lesions that affect all DNA transactions, which in turn can lead to the formation of double-strand breaks, genomic instability and cell death. At the organismal level, impaired DPC repair (DPCR) is associated with cancer, ageing and neurodegeneration. Despite the severe consequences of DPCs, little is known about the processes underlying repair pathways at the organism level. SPRTN is a protease that removes most cellular DPCs during replication, whereas tyrosyl-DNA phosphodiesterase 1 repairs one of the most abundant enzymatic DPCs, topoisomerase 1-DPC (TOP1-DPC). How these two enzymes repair DPCs at the organism level is currently unknown. We perform phylogenetic, syntenic, structural and expression analysis to compare tyrosyl-DNA phosphodiesterase 1 (TDP1) orthologues between human, mouse and zebrafish. Using the zebrafish animal model and human cells, we demonstrate that TDP1 and SPRTN repair endogenous, camptothecin- and formaldehyde-induced DPCs, including histone H3- and TOP1-DPCs. We show that resolution of H3-DNA crosslinks depends on upstream proteolysis by SPRTN and subsequent peptide removal by TDP1 in RPE1 cells and zebrafish embryos, whereas SPRTN and TDP1 function in different pathways in the repair of endogenous TOP1-DPCs and total DPCs. Furthermore, we have found increased TDP2 expression in TDP1-deficient cells and embryos. Understanding the role of TDP1 in DPCR at the cellular and organismal levels could provide an impetus for the development of new drugs and combination therapies with TOP1-DPC inducing drugs.
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Affiliation(s)
- Ivan Anticevic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Cecile Otten
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Vinkovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Jukic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Marta Popovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
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3
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Farahani PE, Nelson CM. Revealing epithelial morphogenetic mechanisms through live imaging. Curr Opin Genet Dev 2022; 72:61-68. [PMID: 34864332 PMCID: PMC8860867 DOI: 10.1016/j.gde.2021.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/08/2021] [Accepted: 10/20/2021] [Indexed: 02/03/2023]
Abstract
Epithelial morphogenesis is guided by mechanical forces and biochemical signals that vary spatiotemporally. As many morphogenetic events are driven by rapid cellular processes, understanding morphogenesis requires monitoring development in real time. Here, we discuss how live-imaging approaches can help identify morphogenetic mechanisms otherwise missed in static snapshots of development. We begin with a summary of live-imaging strategies, including recent advances that push the limits of spatiotemporal resolution and specimen size. We then describe recent efforts that employ live imaging to uncover morphogenetic mechanisms. We conclude by discussing how information collected from live imaging can be enhanced by genetically encoded biosensors and spatiotemporal perturbation techniques to determine the dynamics of patterning of developmental signals and their importance for guiding morphogenesis.
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Affiliation(s)
- Payam E Farahani
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Celeste M Nelson
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, United States; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States.
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4
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Gong F, Shen T, Zhang J, Wang X, Fan G, Che X, Xu Z, Jia K, Huang Y, Li X, Lu H. Nitazoxanide induced myocardial injury in zebrafish embryos by activating oxidative stress response. J Cell Mol Med 2021; 25:9740-9752. [PMID: 34533278 PMCID: PMC8505840 DOI: 10.1111/jcmm.16922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/24/2021] [Accepted: 09/01/2021] [Indexed: 12/20/2022] Open
Abstract
Nitazoxanide (NTZ) is a broad-spectrum antiparasitic and antiviral drug (thiazole). However, although NTZ has been extensively used, there are no reports concerning its toxicology in vertebrates. This study used the zebrafish as a vertebrate model to evaluate the safety of NTZ and to analyse the related molecular mechanisms. The experimental results showed that zebrafish embryos exposed to NTZ had cardiac malformation and dysfunction. NTZ also significantly inhibited proliferation and promoted apoptosis in cardiomyocytes. Transcriptomic analysis used compared gene expression levels between zebrafish embryos in the NTZ treatment and the control groups identified 200 upregulated genes and 232 downregulated genes. Analysis by Kyoto encyclopaedia of genes and genomes (KEGG) and gene ontology (GO) showed that signal pathways on cardiomyocyte development were inhibited while the oxidative stress pathways were activated. Further experiments showed that NTZ increased the content of reactive oxygen species (ROS) in the hearts of zebrafish. Antioxidant gadofullerene nanoparticles (GFNPs) significantly alleviated the developmental toxicity to the heart, indicating that NTZ activated the oxidative stress response to cause embryonic cardiomyocyte injury in zebrafish. This study provides evidence that NTZ causes developmental abnormalities in the cardiovascular system of zebrafish.
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Affiliation(s)
- Fanghua Gong
- School of Pharmacy, Wenzhou Medical University, Wenzhou, China
| | - Tianzhu Shen
- School of Pharmacy, Wenzhou Medical University, Wenzhou, China
| | - Jiangnan Zhang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, China
| | - Xuye Wang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, China
| | - Guoqiang Fan
- School of Pharmacy, Wenzhou Medical University, Wenzhou, China
| | - Xiaofang Che
- Center for drug screening and research, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Zhaopeng Xu
- Center for drug screening and research, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Kun Jia
- Center for drug screening and research, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yong Huang
- Center for drug screening and research, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Xiaokun Li
- School of Pharmacy, Wenzhou Medical University, Wenzhou, China
| | - Huiqiang Lu
- Center for drug screening and research, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, Jiangxi, China.,Jiangxi Engineering laboratory of Zebrafish Modeling and Drug Screening for Human Diseases; Jiangxi Key Laboratory of Developmental Biology of Organs, Ji'an, Jiangxi, China
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5
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Giacomello E, Toniolo L. The Potential of Calorie Restriction and Calorie Restriction Mimetics in Delaying Aging: Focus on Experimental Models. Nutrients 2021; 13:2346. [PMID: 34371855 PMCID: PMC8308705 DOI: 10.3390/nu13072346] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/06/2021] [Accepted: 07/06/2021] [Indexed: 11/17/2022] Open
Abstract
Aging is a biological process determined by multiple cellular mechanisms, such as genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication, that ultimately concur in the functional decline of the individual. The evidence that the old population is steadily increasing and will triplicate in the next 50 years, together with the fact the elderlies are more prone to develop pathologies such as cancer, diabetes, and degenerative disorders, stimulates an important effort in finding specific countermeasures. Calorie restriction (CR) has been demonstrated to modulate nutrient sensing mechanisms, inducing a better metabolic profile, enhanced stress resistance, reduced oxidative stress, and improved inflammatory response. Therefore, CR and CR-mimetics have been suggested as powerful means to slow aging and extend healthy life-span in experimental models and humans. Taking into consideration the difficulties and ethical issues in performing aging research and testing anti-aging interventions in humans, researchers initially need to work with experimental models. The present review reports the major experimental models utilized in the study of CR and CR-mimetics, highlighting their application in the laboratory routine, and their translation to human research.
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Affiliation(s)
- Emiliana Giacomello
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Luana Toniolo
- Laboratory of Muscle Biophysics, Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
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6
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Wang D, Roy S, Rudzite AM, Field GD, Gong Y. High-resolution light-field microscopy with patterned illumination. BIOMEDICAL OPTICS EXPRESS 2021; 12:3887-3901. [PMID: 34457387 PMCID: PMC8367239 DOI: 10.1364/boe.425742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/19/2021] [Accepted: 06/01/2021] [Indexed: 05/21/2023]
Abstract
Light-field fluorescence microscopy can record large-scale population activity of neurons expressing genetically-encoded fluorescent indicators within volumes of tissue. Conventional light-field microscopy (LFM) suffers from poor lateral resolution when using wide-field illumination. Here, we demonstrate a structured-illumination light-field microscopy (SI-LFM) modality that enhances spatial resolution over the imaging volume. This modality increases resolution by illuminating sample volume with grating patterns that are invariant over the axial direction. The size of the SI-LFM point-spread-function (PSF) was approximately half the size of the conventional LFM PSF when imaging fluorescent beads. SI-LFM also resolved fine spatial features in lens tissue samples and fixed mouse retina samples. Finally, SI-LFM reported neural activity with approximately three times the signal-to-noise ratio of conventional LFM when imaging live zebrafish expressing a genetically encoded calcium sensor.
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Affiliation(s)
- Depeng Wang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Suva Roy
- Department of Neurobiology, Duke University, Durham, NC 27708, USA
| | - Andra M Rudzite
- Department of Neurobiology, Duke University, Durham, NC 27708, USA
| | - Greg D Field
- Department of Neurobiology, Duke University, Durham, NC 27708, USA
| | - Yiyang Gong
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Department of Neurobiology, Duke University, Durham, NC 27708, USA
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7
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Andreana M, Sturtzel C, Spielvogel CP, Papp L, Leitgeb R, Drexler W, Distel M, Unterhuber A. Toward Quantitative in vivo Label-Free Tracking of Lipid Distribution in a Zebrafish Cancer Model. Front Cell Dev Biol 2021; 9:675636. [PMID: 34277618 PMCID: PMC8280786 DOI: 10.3389/fcell.2021.675636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/04/2021] [Indexed: 11/26/2022] Open
Abstract
Cancer cells often adapt their lipid metabolism to accommodate the increased fatty acid demand for membrane biogenesis and energy production. Upregulation of fatty acid uptake from the environment of cancer cells has also been reported as an alternative mechanism. To investigate the role of lipids in tumor onset and progression and to identify potential diagnostic biomarkers, lipids are ideally imaged directly within the intact tumor tissue in a label-free way. In this study, we investigated lipid accumulation and distribution in living zebrafish larvae developing a tumor by means of coherent anti-Stokes Raman scattering microscopy. Quantitative textural features based on radiomics revealed higher lipid accumulation in oncogene-expressing larvae compared to healthy ones. This high lipid accumulation could reflect an altered lipid metabolism in the hyperproliferating oncogene-expressing cells.
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Affiliation(s)
- Marco Andreana
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Caterina Sturtzel
- Innovative Cancer Models, St. Anna Children's Cancer Research Institute, Vienna, Austria.,Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Clemens P Spielvogel
- Division of Nuclear Medicine, Department of Medical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria.,Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, Vienna, Austria
| | - Laszlo Papp
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Rainer Leitgeb
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria.,Christian Doppler Laboratory OPTRAMED, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Drexler
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Martin Distel
- Innovative Cancer Models, St. Anna Children's Cancer Research Institute, Vienna, Austria.,Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Angelika Unterhuber
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
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8
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Xie Y, Huang D, Chu L, Liu Y, Sun X, Li J, Cheng CHK. Igf3 is essential for ovary differentiation in zebrafish†. Biol Reprod 2020; 104:589-601. [PMID: 33276384 DOI: 10.1093/biolre/ioaa218] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 12/28/2022] Open
Abstract
Zebrafish gonadal sexual differentiation is an important but poorly understood subject. Previously, we have identified a novel insulin-like growth factor (Igf) named insulin-like growth factor 3 (Igf3) in teleosts. The importance of Igf3 in oocyte maturation and ovulation has been recently demonstrated by us in zebrafish. In this study, we have further found the essential role of Igf3 in gonadal sexual differentiation of zebrafish. A differential expression pattern of igf3 between ovary and testis during sex differentiation (higher level in ovary than in testis) was found in zebrafish. An igf3 knockout zebrafish line was established using TALENs-mediated gene knockout technique. Intriguingly, all igf3 homozygous mutants were males due to the female-to-male sex reversal occurred during sex differentiation. Further analysis showed that Igf3 did not seem to affect the formation of so-called juvenile ovary and oocyte-like germ cells. Oocyte development was arrested at primary growth stage, and the ovary was gradually sex-reversed to testis before 60 day post fertilization (dpf). Such sex reversal was likely due to decreased germ cell proliferation by suppressing PI3K/Akt pathway in early ovaries of igf3 mutants. Estrogen is considered as a master regulator in fish sex differentiation. Here, we found that igf3 expression could be upregulated by estrogen in early stages of ovarian follicles as evidenced in in vitro treatment assays and cyp19a1a mutant zebrafish, and E2 failed to rescue the defects of igf3 mutants in ovarian development, suggesting that Igf3 may serve as a downstream factor of estrogen signaling in sex differentiation. Taken together, we demonstrated that Igf3 is essential for ovary differentiation in zebrafish.
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Affiliation(s)
- Yuxin Xie
- School of Biomedical Sciences, The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Duo Huang
- School of Biomedical Sciences, The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Lianhe Chu
- School of Biomedical Sciences, The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yun Liu
- School of Biomedical Sciences, The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xiao Sun
- School of Biomedical Sciences, The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jianzhen Li
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Christopher H K Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong
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9
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Eastman AE, Guo S. The palette of techniques for cell cycle analysis. FEBS Lett 2020; 594:10.1002/1873-3468.13842. [PMID: 32441778 PMCID: PMC9261528 DOI: 10.1002/1873-3468.13842] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/20/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022]
Abstract
The cell division cycle is the generational period of cellular growth and propagation. Cell cycle progression needs to be highly regulated to preserve genomic fidelity while increasing cell number. In multicellular organisms, the cell cycle must also coordinate with cell fate specification during development and tissue homeostasis. Altered cell cycle dynamics play a central role also in a number of pathophysiological processes. Thus, extensive effort has been made to define the biochemical machineries that execute the cell cycle and their regulation, as well as implementing more sensitive and accurate cell cycle measurements. Here, we review the available techniques for cell cycle analysis, revisiting the assumptions behind conventional population-based measurements and discussing new tools to better address cell cycle heterogeneity in the single-cell era. We weigh the strengths, weaknesses, and trade-offs of methods designed to measure temporal aspects of the cell cycle. Finally, we discuss emerging techniques for capturing cell cycle speed at single-cell resolution in live animals.
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Affiliation(s)
- Anna E Eastman
- Department of Cell Biology and Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Shangqin Guo
- Department of Cell Biology and Yale Stem Cell Center, Yale University, New Haven, CT, USA
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10
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Daetwyler S, Günther U, Modes CD, Harrington K, Huisken J. Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish. Development 2019; 146:dev173757. [PMID: 30824551 PMCID: PMC6451323 DOI: 10.1242/dev.173757] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/18/2019] [Indexed: 01/14/2023]
Abstract
To quantitatively understand biological processes that occur over many hours or days, it is desirable to image multiple samples simultaneously, and automatically process and analyse the resulting datasets. Here, we present a complete multi-sample preparation, imaging, processing and analysis workflow to determine the development of the vascular volume in zebrafish. Up to five live embryos were mounted and imaged simultaneously over several days using selective plane illumination microscopy (SPIM). The resulting large imagery dataset of several terabytes was processed in an automated manner on a high-performance computer cluster and segmented using a novel segmentation approach that uses images of red blood cells as training data. This analysis yielded a precise quantification of growth characteristics of the whole vascular network, head vasculature and tail vasculature over development. Our multi-sample platform demonstrates effective upgrades to conventional single-sample imaging platforms and paves the way for diverse quantitative long-term imaging studies.
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Affiliation(s)
- Stephan Daetwyler
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Ulrik Günther
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Chair of Scientific Computing for Systems Biology, Faculty of Computer Science, TU Dresden, 01069 Dresden, Germany
| | - Carl D Modes
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Kyle Harrington
- Virtual Technology and Design, University of Idaho, Moscow, ID 83844, USA
| | - Jan Huisken
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA
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11
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Chatterjee K, Pratiwi FW, Wu FCM, Chen P, Chen BC. Recent Progress in Light Sheet Microscopy for Biological Applications. APPLIED SPECTROSCOPY 2018; 72:1137-1169. [PMID: 29926744 DOI: 10.1177/0003702818778851] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The introduction of light sheet fluorescence microscopy (LSFM) has overcome the challenges in conventional optical microscopy. Among the recent breakthroughs in fluorescence microscopy, LSFM had been proven to provide a high three-dimensional spatial resolution, high signal-to-noise ratio, fast imaging acquisition rate, and minuscule levels of phototoxic and photodamage effects. The aforementioned auspicious properties are crucial in the biomedical and clinical research fields, covering a broad range of applications: from the super-resolution imaging of intracellular dynamics in a single cell to the high spatiotemporal resolution imaging of developmental dynamics in an entirely large organism. In this review, we provided a systematic outline of the historical development of LSFM, detailed discussion on the variants and improvements of LSFM, and delineation on the most recent technological advancements of LSFM and its potential applications in single molecule/particle detection, single-molecule super-resolution imaging, imaging intracellular dynamics of a single cell, multicellular imaging: cell-cell and cell-matrix interactions, plant developmental biology, and brain imaging and developmental biology.
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Affiliation(s)
- Krishnendu Chatterjee
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 3 Department of Engineering and System Science, National Tsing-Hua University, Hsinchu, Taiwan
| | - Feby Wijaya Pratiwi
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 4 Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | | | - Peilin Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
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12
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Abstract
Three-dimensional (3D) cell culture systems have gained increasing interest not only for 3D migration studies but also for their use in drug screening, tissue engineering, and ex vivo modeling of metastatic behavior in the field of cancer biology and morphogenesis in the field of developmental biology. The goal of studying cells in a 3D context is to attempt to more faithfully recapitulate the physiological microenvironment of tissues, including mechanical and structural parameters that we envision will reveal more predictive data for development programs and disease states. In this review, we discuss the pros and cons of several well-characterized 3D cell culture systems for performing 3D migration studies. We discuss the intracellular and extracellular signaling mechanisms that govern cell migration. We also describe the mathematical models and relevant assumptions that can be used to describe 3D cell movement.
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Affiliation(s)
- Pei-Hsun Wu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences in Oncology Center, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA;, ,
| | - Daniele M. Gilkes
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences in Oncology Center, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA;, ,
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Denis Wirtz
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences in Oncology Center, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA;, ,
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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13
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Abstract
In recent years, use of the zebrafish embryo as a model organism to study vascular development in vivo has provided valuable insights into the genetic and cellular events shaping the embryonic vasculature. In this chapter, we aim to present the methods for the measurement of some of the most commonly investigated dynamic parameters in endothelial cells during developmental angiogenesis, namely, migration speed and acceleration, filopodia extension, front-rear polarity, cell cycle progression, membrane deformations, and junctional rearrangements. We also offer suggestions on how to deal with the most common imaging and quantifications challenges faced when acquiring and quantifying endothelial cell dynamic behavior in vivo.We intend this section to serve as an experience-based imaging primer for scientists interested in endothelial cell imaging in the zebrafish embryo.
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Affiliation(s)
- Baptiste Coxam
- Integrative Vascular Biology Laboratory, Max-Delbrück Center for Molecular Medicine (MDC), Berlin, Germany.
- DZHK (German Center for Cardiovascular Research), Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
| | - Holger Gerhardt
- Integrative Vascular Biology Laboratory, Max-Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Vascular Patterning Laboratory, Vesalius Research Center, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
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14
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Wellmann J. Animating embryos: the in toto representation of life. BRITISH JOURNAL FOR THE HISTORY OF SCIENCE 2017; 50:521-535. [PMID: 28923124 DOI: 10.1017/s0007087417000656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
With the recent advent of systems biology, developmental biology is taking a new turn. Attempts to create a 'digital embryo' are prominent among systems approaches. At the heart of these systems-based endeavours, variously described as 'in vivo imaging', 'live imaging' or 'in toto representation', are visualization techniques that allow researchers to image whole, live embryos at cellular resolution over time. Ultimately, the aim of the visualizations is to build a computer model of embryogenesis. This article examines the role of such visualization techniques in the building of a computational model, focusing, in particular, on the cinematographic character of these representations. It asks how the animated representation of development may change the biological understanding of embryogenesis. By situating the animations of the digital embryo within the iconography of developmental biology, it brings to light the inextricably entwined, yet shifting, borders between the animated, the living and the computational.
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Affiliation(s)
- Janina Wellmann
- *Institute for Advanced Study on Media Cultures of Computer Simulation,Leuphana University Lüneburg,Wallstr.3,21335 Lüneburg,Germany.
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15
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Xin X, Clark D, Ang KC, van Rossum DB, Copper J, Xiao X, La Riviere PJ, Cheng KC. Synchrotron microCT imaging of soft tissue in juvenile zebrafish reveals retinotectal projections. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2017; 10060. [PMID: 32733117 DOI: 10.1117/12.2267477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Biomedical research and clinical diagnosis would benefit greatly from full volume determinations of anatomical phenotype. Comprehensive tools for morphological phenotyping are central for the emerging field of phenomics, which requires high-throughput, systematic, accurate, and reproducible data collection from organisms affected by genetic, disease, or environmental variables. Theoretically, complete anatomical phenotyping requires the assessment of every cell type in the whole organism, but this ideal is presently untenable due to the lack of an unbiased 3D imaging method that allows histopathological assessment of any cell type despite optical opacity. Histopathology, the current clinical standard for diagnostic phenotyping, involves the microscopic study of tissue sections to assess qualitative aspects of tissue architecture, disease mechanisms, and physiological state. However, quantitative features of tissue architecture such as cellular composition and cell counting in tissue volumes can only be approximated due to characteristics of tissue sectioning, including incomplete sampling and the constraints of 2D imaging of 5 micron thick tissue slabs. We have used a small, vertebrate organism, the zebrafish, to test the potential of microCT for systematic macroscopic and microscopic morphological phenotyping. While cell resolution is routinely achieved using methods such as light sheet fluorescence microscopy and optical tomography, these methods do not provide the pancellular perspective characteristic of histology, and are constrained by the limited penetration of visible light through pigmented and opaque specimens, as characterizes zebrafish juveniles. Here, we provide an example of neuroanatomy that can be studied by microCT of stained soft tissue at 1.43 micron isotropic voxel resolution. We conclude that synchrotron microCT is a form of 3D imaging that may potentially be adopted towards more reproducible, large-scale, morphological phenotyping of optically opaque tissues. Further development of soft tissue microCT, visualization and quantitative tools will enhance its utility.
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Affiliation(s)
- Xuying Xin
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.,Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.,Penn State Consortium for Interdisciplinary Image Informatics and Visualization, USA
| | - Darin Clark
- Center for In Vivo Microscopy, Department of Radiology, Duke University Medical Center, Durham, NC 27708, USA
| | - Khai Chung Ang
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.,Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.,Penn State Consortium for Interdisciplinary Image Informatics and Visualization, USA
| | - Damian B van Rossum
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.,Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.,Penn State Consortium for Interdisciplinary Image Informatics and Visualization, USA
| | - Jean Copper
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.,Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.,Penn State Consortium for Interdisciplinary Image Informatics and Visualization, USA
| | - Xianghui Xiao
- Advanced Photon Source, Argonne National Laboratory Argonne, IL 60439, USA
| | | | - Keith C Cheng
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.,Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.,Penn State Consortium for Interdisciplinary Image Informatics and Visualization, USA
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16
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Baxendale S, van Eeden F, Wilkinson R. The Power of Zebrafish in Personalised Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:179-197. [PMID: 28840558 DOI: 10.1007/978-3-319-60733-7_10] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The goal of personalised medicine is to develop tailor-made therapies for patients in whom currently available therapeutics fail. This approach requires correlating individual patient genotype data to specific disease phenotype data and using these stratified data sets to identify bespoke therapeutics. Applications for personalised medicine include common complex diseases which may have multiple targets, as well as rare monogenic disorders, for which the target may be unknown. In both cases, whole genome sequence analysis (WGS) is discovering large numbers of disease associated mutations in new candidate genes and potential modifier genes. Currently, the main limiting factor is the determination of which mutated genes are important for disease progression and therefore represent potential targets for drug discovery. Zebrafish have gained popularity as a model organism for understanding developmental processes, disease mechanisms and more recently for drug discovery and toxicity testing. In this chapter, we will examine the diverse roles that zebrafish can make in the expanding field of personalised medicine, from generating humanised disease models to xenograft screening of different cancer cell lines, through to finding new drugs via in vivo phenotypic screens. We will discuss the tools available for zebrafish research and recent advances in techniques, highlighting the advantages and potential of using zebrafish for high throughput disease modeling and precision drug discovery.
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Affiliation(s)
- Sarah Baxendale
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Freek van Eeden
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert Wilkinson
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK.,Department of Infection, Immunity and Cardiovascular Disease, Medical School, Beech Hill Rd, University of Sheffield, Sheffield, S10 2RX, UK
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17
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Grist SM, Nasseri SS, Poon T, Roskelley C, Cheung KC. On-chip clearing of arrays of 3-D cell cultures and micro-tissues. BIOMICROFLUIDICS 2016; 10:044107. [PMID: 27493703 PMCID: PMC4958101 DOI: 10.1063/1.4959031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/06/2016] [Indexed: 05/16/2023]
Abstract
Three-dimensional (3-D) cell cultures are beneficial models for mimicking the complexities of in vivo tissues, especially in tumour studies where transport limitations can complicate response to cancer drugs. 3-D optical microscopy techniques are less involved than traditional embedding and sectioning, but are impeded by optical scattering properties of the tissues. Confocal and even two-photon microscopy limit sample imaging to approximately 100-200 μm depth, which is insufficient to image hypoxic spheroid cores. Optical clearing methods have permitted high-depth imaging of tissues without physical sectioning, but they are difficult to implement for smaller 3-D cultures due to sample loss in solution exchange. In this work, we demonstrate a microfluidic platform for high-throughput on-chip optical clearing of breast cancer spheroids using the SeeDB, Clear(T2), and ScaleSQ clearing methods. Although all three methods are able to effectively clear the spheroids, we find that SeeDB and ScaleSQ more effectively clear the sample than Clear(T2); however, SeeDB induces green autofluorescence while ScaleS causes sample expansion. Our unique on-chip implementation permits clearing arrays of 3-D cultures using perfusion while monitoring the 3-D cultures throughout the process, enabling visualization of the clearing endpoint as well as monitoring of transient changes that could induce image artefacts. Our microfluidic device is compatible with on-chip 3-D cell culture, permitting the use of on-chip clearing at the endpoint after monitoring the same spheroids during their culture. This on-chip method has the potential to improve readout from 3-D cultures, facilitating their use in cell-based assays for high-content drug screening and other applications.
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Affiliation(s)
- S M Grist
- Department of Electrical and Computer Engineering, The University of British Columbia , 2332 Main Mall, Vancouver, BC Canada V6T 1Z4
| | - S S Nasseri
- Department of Electrical and Computer Engineering, The University of British Columbia , 2332 Main Mall, Vancouver, BC Canada V6T 1Z4
| | - T Poon
- Department of Cellular and Physiological Sciences, The University of British Columbia , 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
| | - C Roskelley
- Department of Cellular and Physiological Sciences, The University of British Columbia , 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
| | - K C Cheung
- Department of Electrical and Computer Engineering, The University of British Columbia , 2332 Main Mall, Vancouver, BC Canada V6T 1Z4
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18
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S. C, C. C, T. M, G. S, N. R. Biosurfactant templated quantum sized fluorescent gold nanoclusters for in vivo bioimaging in zebrafish embryos. Colloids Surf B Biointerfaces 2016; 143:472-480. [DOI: 10.1016/j.colsurfb.2016.03.067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/17/2022]
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19
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White DE, Sylvester JB, Levario TJ, Lu H, Streelman JT, McDevitt TC, Kemp ML. Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories. Integr Biol (Camb) 2016; 7:825-33. [PMID: 26095427 DOI: 10.1039/c5ib00072f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Interrogating fundamental cell biology principles that govern tissue morphogenesis is critical to better understanding of developmental biology and engineering novel multicellular systems. Recently, functional micro-tissues derived from pluripotent embryonic stem cell (ESC) aggregates have provided novel platforms for experimental investigation; however elucidating the factors directing emergent spatial phenotypic patterns remains a significant challenge. Computational modelling techniques offer a unique complementary approach to probe mechanisms regulating morphogenic processes and provide a wealth of spatio-temporal data, but quantitative analysis of simulations and comparison to experimental data is extremely difficult. Quantitative descriptions of spatial phenomena across multiple systems and scales would enable unprecedented comparisons of computational simulations with experimental systems, thereby leveraging the inherent power of computational methods to interrogate the mechanisms governing emergent properties of multicellular biology. To address these challenges, we developed a portable pattern recognition pipeline consisting of: the conversion of cellular images into networks, extraction of novel features via network analysis, and generation of morphogenic trajectories. This novel methodology enabled the quantitative description of morphogenic pattern trajectories that could be compared across diverse systems: computational modelling of multicellular structures, differentiation of stem cell aggregates, and gastrulation of cichlid fish. Moreover, this method identified novel spatio-temporal features associated with different stages of embryo gastrulation, and elucidated a complex paracrine mechanism capable of explaining spatiotemporal pattern kinetic differences in ESC aggregates of different sizes.
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Affiliation(s)
- Douglas E White
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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20
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Park OK, Kwak J, Jung YJ, Kim YH, Hong HS, Hwang BJ, Kwon SH, Kee Y. 3D Light-Sheet Fluorescence Microscopy of Cranial Neurons and Vasculature during Zebrafish Embryogenesis. Mol Cells 2015; 38:975-81. [PMID: 26429501 PMCID: PMC4673412 DOI: 10.14348/molcells.2015.0160] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/16/2015] [Accepted: 07/30/2015] [Indexed: 11/27/2022] Open
Abstract
Precise 3D spatial mapping of cells and their connections within living tissues is required to fully understand developmental processes and neural activities. Zebrafish embryos are relatively small and optically transparent, making them the vertebrate model of choice for live in vivo imaging. However, embryonic brains cannot be imaged in their entirety by confocal or two-photon microscopy due to limitations in optical range and scanning speed. Here, we use light-sheet fluorescence microscopy to overcome these limitations and image the entire head of live transgenic zebrafish embryos. We simultaneously imaged cranial neurons and blood vessels during embryogenesis, generating comprehensive 3D maps that provide insight into the coordinated morphogenesis of the nervous system and vasculature during early development. In addition, blood cells circulating through the entire head, vagal and cardiac vasculature were also visualized at high resolution in a 3D movie. These data provide the foundation for the construction of a complete 4D atlas of zebrafish embryogenesis and neural activity.
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Affiliation(s)
- Ok Kyu Park
- Korea Basic Science Institute Chuncheon Center, Chuncheon 200-701,
Korea
| | - Jina Kwak
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701,
Korea
| | - Yoo Jung Jung
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701,
Korea
| | | | | | - Byung Joon Hwang
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 200-701,
Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 200-701,
Korea
| | - Seung-Hae Kwon
- Korea Basic Science Institute Chuncheon Center, Chuncheon 200-701,
Korea
| | - Yun Kee
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701,
Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 200-701,
Korea
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21
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Lim J, Lee HK, Yu W, Ahmed S. Light sheet fluorescence microscopy (LSFM): past, present and future. Analyst 2015; 139:4758-68. [PMID: 25118817 DOI: 10.1039/c4an00624k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light sheet fluorescence microscopy (LSFM) has emerged as an important imaging modality to follow biology in live 3D samples over time with reduced phototoxicity and photobleaching. In particular, LSFM has been instrumental in revealing the detail of early embryonic development of Zebrafish, Drosophila, and C. elegans. Open access projects, DIY-SPIM, OpenSPIM, and OpenSPIN, now allow LSFM to be set-up easily and at low cost. The aim of this paper is to facilitate the set-up and use of LSFM by reviewing and comparing open access projects, image processing tools and future challenges.
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Affiliation(s)
- John Lim
- Institute of Medical Biology, 8A Biomedical Grove, Immunos 5.37, Singapore 138648, Singapore.
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22
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Kang YF, Li YH, Fang YW, Xu Y, Wei XM, Yin XB. Carbon Quantum Dots for Zebrafish Fluorescence Imaging. Sci Rep 2015; 5:11835. [PMID: 26135470 PMCID: PMC4488761 DOI: 10.1038/srep11835] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/30/2015] [Indexed: 12/23/2022] Open
Abstract
Carbon quantum dots (C-QDs) are becoming a desirable alternative to metal-based QDs and dye probes owing to their high biocompatibility, low toxicity, ease of preparation, and unique photophysical properties. Herein, we describe fluorescence bioimaging of zebrafish using C-QDs as probe in terms of the preparation of C-QDs, zebrafish husbandry, embryo harvesting, and introduction of C-QDs into embryos and larvae by soaking and microinjection. The multicolor of C-QDs was validated with their imaging for zebrafish embryo. The distribution of C-QDs in zebrafish embryos and larvae were successfully observed from their fluorescence emission. the bio-toxicity of C-QDs was tested with zebrafish as model and C-QDs do not interfere to the development of zebrafish embryo. All of the results confirmed the high biocompatibility and low toxicity of C-QDs as imaging probe. The absorption, distribution, metabolism and excretion route (ADME) of C-QDs in zebrafish was revealed by their distribution. Our work provides the useful information for the researchers interested in studying with zebrafish as a model and the applications of C-QDs. The operations related zebrafish are suitable for the study of the toxicity, adverse effects, transport, and biocompatibility of nanomaterials as well as for drug screening with zebrafish as model.
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Affiliation(s)
- Yan-Fei Kang
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin Key laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
| | - Yu-Hao Li
- Tianjin Key Laboratory of Tumor Microenviroment and Neurovascular Regulation, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yang-Wu Fang
- Tianjin Key Laboratory of Tumor Microenviroment and Neurovascular Regulation, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yang Xu
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin Key laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
| | - Xiao-Mi Wei
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin Key laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
| | - Xue-Bo Yin
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin Key laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
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23
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Jungke P, Hammer J, Hans S, Brand M. Isolation of Novel CreERT2-Driver Lines in Zebrafish Using an Unbiased Gene Trap Approach. PLoS One 2015; 10:e0129072. [PMID: 26083735 PMCID: PMC4471347 DOI: 10.1371/journal.pone.0129072] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 05/04/2015] [Indexed: 01/01/2023] Open
Abstract
Gene manipulation using the Cre/loxP-recombinase system has been successfully employed in zebrafish to study gene functions and lineage relationships. Recently, gene trapping approaches have been applied to produce large collections of transgenic fish expressing conditional alleles in various tissues. However, the limited number of available cell- and tissue-specific Cre/CreERT2-driver lines still constrains widespread application in this model organism. To enlarge the pool of existing CreERT2-driver lines, we performed a genome-wide gene trap screen using a Tol2-based mCherry-T2a-CreERT2 (mCT2aC) gene trap vector. This cassette consists of a splice acceptor and a mCherry-tagged variant of CreERT2 which enables simultaneous labeling of the trapping event, as well as CreERT2 expression from the endogenous promoter. Using this strategy, we generated 27 novel functional CreERT2-driver lines expressing in a cell- and tissue-specific manner during development and adulthood. This study summarizes the analysis of the generated CreERT2-driver lines with respect to functionality, expression, integration, as well as associated phenotypes. Our results significantly enlarge the existing pool of CreERT2-driver lines in zebrafish and combined with Cre-dependent effector lines, the new CreERT2-driver lines will be important tools to manipulate the zebrafish genome.
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Affiliation(s)
- Peggy Jungke
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Juliane Hammer
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Stefan Hans
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Michael Brand
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
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24
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Mitchell TJ, Saunter CD, O'Nions W, Girkin JM, Love GD. Quantitative high dynamic range beam profiling for fluorescence microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:103713. [PMID: 25362409 DOI: 10.1063/1.4899208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Modern developmental biology relies on optically sectioning fluorescence microscope techniques to produce non-destructive in vivo images of developing specimens at high resolution in three dimensions. As optimal performance of these techniques is reliant on the three-dimensional (3D) intensity profile of the illumination employed, the ability to directly record and analyze these profiles is of great use to the fluorescence microscopist or instrument builder. Though excitation beam profiles can be measured indirectly using a sample of fluorescent beads and recording the emission along the microscope detection path, we demonstrate an alternative approach where a miniature camera sensor is used directly within the illumination beam. Measurements taken using our approach are solely concerned with the illumination optics as the detection optics are not involved. We present a miniature beam profiling device and high dynamic range flux reconstruction algorithm that together are capable of accurately reproducing quantitative 3D flux maps over a large focal volume. Performance of this beam profiling system is verified within an optical test bench and demonstrated for fluorescence microscopy by profiling the low NA illumination beam of a single plane illumination microscope. The generality and success of this approach showcases a widely flexible beam amplitude diagnostic tool for use within the life sciences.
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Affiliation(s)
- T J Mitchell
- Centre for Advanced Instrumentation and Biophysical Sciences Institute, Department of Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - C D Saunter
- Centre for Advanced Instrumentation and Biophysical Sciences Institute, Department of Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - W O'Nions
- Centre for Advanced Instrumentation and Biophysical Sciences Institute, Department of Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - J M Girkin
- Centre for Advanced Instrumentation and Biophysical Sciences Institute, Department of Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - G D Love
- Centre for Advanced Instrumentation and Biophysical Sciences Institute, Department of Physics, Durham University, Durham DH1 3LE, United Kingdom
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25
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Purnapatra SB, Mohan K, Mondal PP. Generation of multiple sheets of light using spatial-filtering technique. OPTICS LETTERS 2014; 39:4715-4718. [PMID: 25121856 DOI: 10.1364/ol.39.004715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We develop an optical system for generating multiple light sheets. This is enabled by employing a special class of spatial filters in a cylindrical lens geometry. The proposed binary filter placed at the back aperture of the cylindrical lens results in the generation of a periodic transverse pattern extending along the z axis (i.e., multiple light sheets). Experimental results confirm the generation of multiple light sheets of thickness 6.6 μm with an intersheet spacing of 13.4 μm. The proposed imaging technique may facilitate three-dimensional imaging in nano-optics, fluorescence microscopy, and nanobiology.
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26
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Fickentscher R, Struntz P, Weiss M. Mechanical cues in the early embryogenesis of Caenorhabditis elegans. Biophys J 2014; 105:1805-11. [PMID: 24138856 DOI: 10.1016/j.bpj.2013.09.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/08/2013] [Accepted: 09/11/2013] [Indexed: 12/21/2022] Open
Abstract
Biochemical signaling pathways in developmental processes have been extensively studied, yet the role of mechanical cues during embryogenesis is much less explored. Here we have used selective plane illumination microscopy in combination with a simple mechanical model to quantify and rationalize cell motion during early embryogenesis of the small nematode Caenorhabditis elegans. As a result, we find that cell organization in the embryo until gastrulation is well described by a purely mechanical model that predicts cells to assume positions in which they face the least repulsive interactions from other cells and the embryo's egg shell. Our findings therefore suggest that mechanical interactions are key for a rapid and robust cellular arrangement during early embryogenesis of C. elegans.
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27
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Ichikawa T, Nakazato K, Keller PJ, Kajiura-Kobayashi H, Stelzer EHK, Mochizuki A, Nonaka S. Live imaging and quantitative analysis of gastrulation in mouse embryos using light-sheet microscopy and 3D tracking tools. Nat Protoc 2014; 9:575-85. [PMID: 24525751 DOI: 10.1038/nprot.2014.035] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes how to observe gastrulation in living mouse embryos by using light-sheet microscopy and computational tools to analyze the resulting image data at the single-cell level. We describe a series of techniques needed to image the embryos under physiological conditions, including how to hold mouse embryos without agarose embedding, how to transfer embryos without air exposure and how to construct environmental chambers for live imaging by digital scanned light-sheet microscopy (DSLM). Computational tools include manual and semiautomatic tracking programs that are developed for analyzing the large 4D data sets acquired with this system. Note that this protocol does not include details of how to build the light-sheet microscope itself. Time-lapse imaging ends within 12 h, with subsequent tracking analysis requiring 3-6 d. Other than some mouse-handling skills, this protocol requires no advanced skills or knowledge. Light-sheet microscopes are becoming more widely available, and thus the techniques outlined in this paper should be helpful for investigating mouse embryogenesis.
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Affiliation(s)
- Takehiko Ichikawa
- Laboratory for Spatiotemporal Regulations, National Institute for Basic Biology, Okazaki Aichi, Japan
| | - Kenichi Nakazato
- Theoretical Biology Laboratory, RIKEN Advanced Science Institute, Wako-city, Japan
| | - Philipp J Keller
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Hiroko Kajiura-Kobayashi
- Laboratory for Spatiotemporal Regulations, National Institute for Basic Biology, Okazaki Aichi, Japan
| | - Ernst H K Stelzer
- Buchmann Institute for Molecular Life Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Atsushi Mochizuki
- Theoretical Biology Laboratory, RIKEN Advanced Science Institute, Wako-city, Japan
| | - Shigenori Nonaka
- Laboratory for Spatiotemporal Regulations, National Institute for Basic Biology, Okazaki Aichi, Japan
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28
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Xu Y, Li YH, Wang Y, Cui JL, Yin XB, He XW, Zhang YK. 13C-engineered carbon quantum dots for in vivo magnetic resonance and fluorescence dual-response. Analyst 2014; 139:5134-9. [DOI: 10.1039/c4an01194e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
13C-engineered carbon quantum dots (13C-QDs) were used as magnetic resonance (MR) and fluorescence dual-response probe.
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Affiliation(s)
- Yang Xu
- State Key Laboratory of Medicinal Chemical Biology
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yu-Hao Li
- Key Laboratory of Animal Models and Degenerative Neurological Diseases (Tianjin)
- School of Medicine
- Nankai University
- Tianjin, China
| | - Yue Wang
- Key Laboratory of Animal Models and Degenerative Neurological Diseases (Tianjin)
- School of Medicine
- Nankai University
- Tianjin, China
| | - Jian-Lin Cui
- Key Laboratory of Animal Models and Degenerative Neurological Diseases (Tianjin)
- School of Medicine
- Nankai University
- Tianjin, China
| | - Xue-Bo Yin
- State Key Laboratory of Medicinal Chemical Biology
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Xi-Wen He
- State Key Laboratory of Medicinal Chemical Biology
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yu-Kui Zhang
- State Key Laboratory of Medicinal Chemical Biology
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
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Lemon WC, Keller PJ. Live imaging of nervous system development and function using light-sheet microscopy. Mol Reprod Dev 2013; 82:605-18. [PMID: 23996352 DOI: 10.1002/mrd.22258] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 08/21/2013] [Indexed: 12/21/2022]
Abstract
In vivo imaging applications typically require carefully balancing conflicting parameters. Often it is necessary to achieve high imaging speed, low photo-bleaching, and photo-toxicity, good three-dimensional resolution, high signal-to-noise ratio, and excellent physical coverage at the same time. Light-sheet microscopy provides good performance in all of these categories, and is thus emerging as a particularly powerful live imaging method for the life sciences. We see an outstanding potential for applying light-sheet microscopy to the study of development and function of the early nervous system in vertebrates and higher invertebrates. Here, we review state-of-the-art approaches to live imaging of early development, and show how the unique capabilities of light-sheet microscopy can further advance our understanding of the development and function of the nervous system. We discuss key considerations in the design of light-sheet microscopy experiments, including sample preparation and fluorescent marker strategies, and provide an outlook for future directions in the field.
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Affiliation(s)
- William C Lemon
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia
| | - Philipp J Keller
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia
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