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Shen YJ, Liao EY, Tai TM, Liao YH, Sun CK, Lee CK, See S, Chen HW. Deep learning-based photodamage reduction on harmonic generation microscope at low-level optical power. JOURNAL OF BIOPHOTONICS 2024; 17:e202300285. [PMID: 37738103 DOI: 10.1002/jbio.202300285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
The trade-off between high-quality images and cellular health in optical bioimaging is a crucial problem. We demonstrated a deep-learning-based power-enhancement (PE) model in a harmonic generation microscope (HGM), including second harmonic generation (SHG) and third harmonic generation (THG). Our model can predict high-power HGM images from low-power images, greatly reducing the risk of phototoxicity and photodamage. Furthermore, the PE model trained only on normal skin data can also be used to predict abnormal skin data, enabling the dermatopathologist to successfully identify and label cancer cells. The PE model shows potential for in-vivo and ex-vivo HGM imaging.
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Affiliation(s)
- Yi-Jiun Shen
- International Intercollegiate Ph.D. Program, National Tsing Hua University, Hsinchu, Taiwan
| | - En-Yu Liao
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei, Taiwan
| | | | - Yi-Hua Liao
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chi-Kuang Sun
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei, Taiwan
| | | | - Simon See
- NVIDIA AI Technology Center, NVIDIA, Taipei, Taiwan
| | - Hung-Wen Chen
- International Intercollegiate Ph.D. Program, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan
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2
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Sung M, Kim JH, Min HS, Jang S, Hong J, Choi BK, Shin J, Chung KS, Park YR. Three-dimensional label-free morphology of CD8 + T cells as a sepsis biomarker. LIGHT, SCIENCE & APPLICATIONS 2023; 12:265. [PMID: 37932249 PMCID: PMC10628166 DOI: 10.1038/s41377-023-01309-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/20/2023] [Accepted: 10/13/2023] [Indexed: 11/08/2023]
Abstract
Sepsis is a dysregulated immune response to infection that leads to organ dysfunction and is associated with a high incidence and mortality rate. The lack of reliable biomarkers for diagnosing and prognosis of sepsis is a major challenge in its management. We aimed to investigate the potential of three-dimensional label-free CD8 + T cell morphology as a biomarker for sepsis. This study included three-time points in the sepsis recovery cohort (N = 8) and healthy controls (N = 20). Morphological features and spatial distribution within cells were compared among the patients' statuses. We developed a deep learning model to predict the diagnosis and prognosis of sepsis using the internal cell morphology. Correlation between the morphological features and clinical indices were analysed. Cell morphological features and spatial distribution differed significantly between patients with sepsis and healthy controls and between the survival and non-survival groups. The model for predicting the diagnosis and prognosis of sepsis showed an area under the receiver operating characteristic curve of nearly 100% with only a few cells, and a strong correlation between the morphological features and clinical indices was observed. Our study highlights the potential of three-dimensional label-free CD8 + T cell morphology as a promising biomarker for sepsis. This approach is rapid, requires a minimum amount of blood samples, and has the potential to provide valuable information for the early diagnosis and prognosis of sepsis.
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Affiliation(s)
- MinDong Sung
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hyun Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun-Seok Min
- Tomocube, Inc, 155 Sinseong-ro, Shinsung-dong, Yuseong-gu, Daejeon, Republic of Korea
| | - Sooyoung Jang
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - JaeSeong Hong
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Bo Kyu Choi
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - JuHye Shin
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyung Soo Chung
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Yu Rang Park
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea.
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3
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Near single-photon imaging in the shortwave infrared using homodyne detection. Proc Natl Acad Sci U S A 2023; 120:e2216678120. [PMID: 36857346 PMCID: PMC10013842 DOI: 10.1073/pnas.2216678120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Low-light imaging is challenging in regimes where low-noise detectors are not yet available. One such regime is the shortwave infrared where even the best multipixel detector arrays typically have a noise floor in excess of 100 photons per pixel per frame. We present a homodyne imaging system capable of recovering both intensity and phase images of an object from a single frame despite an illumination intensity of ≈1 photon per pixel. We interfere this weak signal which is below the noise floor of the detector with a reference beam that is ∼300, 000 times brighter, record the resulting interference pattern in the spatial domain on a detector array, and use Fourier techniques to extract the intensity and phase images. We believe our approach could vastly extend the range of applications for low-light imaging by accessing domains where low-noise cameras are not currently available and for which low-intensity illumination is required.
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4
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Sonoi R, Hagihara Y. Quantitative understanding of HepaRG cells during drug-induced intrahepatic cholestasis through changes in bile canaliculi dynamics. Pharmacol Res Perspect 2022; 10:e00960. [PMID: 35621230 PMCID: PMC9137115 DOI: 10.1002/prp2.960] [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: 02/22/2022] [Accepted: 04/18/2022] [Indexed: 11/09/2022] Open
Abstract
An understanding of the quantitative relationship between bile canaliculus (BC) dynamics and the disruption of tight junctions (TJs) during drug-induced intrahepatic cholestasis may lead to new strategies aimed at drug development and toxicity testing. To investigate the relationship between BC dynamics and TJ disruption, we retrospectively analyzed the extent of TJ disruption in response to changes in the dynamics of BCs cultured with entacapone (ENT). Three hours after adding ENT, the ZO-1-negative BC surface area ratio became significantly higher (4.1-fold) than those of ZO-1-positive BCs. Based on these data, we calculated slopes of surface area changes, m, of each ZO-1-positive and ZO-1-negative BC. BCs with m ≤ 15 that fell within the 95% confidence interval of ZO-1-positive BCs were defined as ZO-1-positive. To validate this method, we compared the frequency of ZO-1-positive BCs, FZ , with that of BCs with m ≤ 15, FT , in culture using drugs that regulate TJ, or induce intrahepatic cholestasis. FT values were correlated with FZ under all culture conditions (R2 = .99). Our results indicate that the magnitude of BC surface area changes is a factor affecting TJ disruption, suggesting that maintaining TJ integrity by slowing BC dilation inhibits cell death.
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Affiliation(s)
- Rie Sonoi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka, Japan
| | - Yoshihisa Hagihara
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka, Japan
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5
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Reiche MA, Aaron JS, Boehm U, DeSantis MC, Hobson CM, Khuon S, Lee RM, Chew TL. When light meets biology - how the specimen affects quantitative microscopy. J Cell Sci 2022; 135:274812. [PMID: 35319069 DOI: 10.1242/jcs.259656] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fluorescence microscopy images should not be treated as perfect representations of biology. Many factors within the biospecimen itself can drastically affect quantitative microscopy data. Whereas some sample-specific considerations, such as photobleaching and autofluorescence, are more commonly discussed, a holistic discussion of sample-related issues (which includes less-routine topics such as quenching, scattering and biological anisotropy) is required to appropriately guide life scientists through the subtleties inherent to bioimaging. Here, we consider how the interplay between light and a sample can cause common experimental pitfalls and unanticipated errors when drawing biological conclusions. Although some of these discrepancies can be minimized or controlled for, others require more pragmatic considerations when interpreting image data. Ultimately, the power lies in the hands of the experimenter. The goal of this Review is therefore to survey how biological samples can skew quantification and interpretation of microscopy data. Furthermore, we offer a perspective on how to manage many of these potential pitfalls.
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Affiliation(s)
- Michael A Reiche
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Jesse S Aaron
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Ulrike Boehm
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Michael C DeSantis
- Light Microscopy Facility, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147,USA
| | - Chad M Hobson
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Satya Khuon
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA.,Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Rachel M Lee
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA.,Light Microscopy Facility, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147,USA
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Emon MAB, Knoll S, Doha U, Ladehoff L, Lalonde L, Baietto D, Sivaguru M, Bhargava R, Saif MTA. Dose- independent threshold illumination for non-invasive time-lapse fluorescence imaging of live cells. EXTREME MECHANICS LETTERS 2021; 46:101249. [PMID: 34095408 PMCID: PMC8171180 DOI: 10.1016/j.eml.2021.101249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Fluorescent microscopy employs monochromatic light for excitation, which can adversely affect the cells being observed. We reported earlier that fibroblasts relax their contractile force in response to green light of typical intensity. Here we show that such effects are independent of extracellular matrix and cell lines. In addition, we establish a threshold intensity that elicits minimal or no adverse effect on cell contractility even for long-time exposure. This threshold intensity is wavelength dependent. We cultured fibroblasts on soft 2D elastic hydrogels embedded with fluorescent beads to trace substrate deformation and cell forces. The beads move towards cell center when cells contract, but they move away when cells relax. We use relaxation/contraction ratio (λ r), in addition to traction force, as measures of cell response to red (wavelength, λ=635-650 nm), green (λ=545-580 nm) and blue (λ=455-490 nm) lights with varying intensities. Our results suggest that intensities below 57, 31 and 3.5 W/m2 for red, green and blue lights, respectively, do not perturb force homeostasis. To our knowledge, these intensities are the lowest reported safe thresholds, implying that cell traction is a highly sensitive readout of the effect of light on cells. Most importantly, we find these threshold intensities to be dose-independent; i.e., safe regardless of the energy dosage or time of exposure. Conversely, higher intensities result in widespread force-relaxation in cells with λ r > 1. Furthermore, we present a photo-reaction based model that simulates photo-toxicity and predicts threshold intensity for different wavelengths within the visible spectra. In conclusion, we recommend employing illumination intensities below aforementioned wavelength-specific thresholds for time-lapse imaging of cells and tissues in order to avoid light-induced artifacts in experimental observations.
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Affiliation(s)
- M A Bashar Emon
- Dept. of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign
| | - Samantha Knoll
- Dept. of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign
| | - Umnia Doha
- Dept. of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign
| | - Lauren Ladehoff
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign
| | - Luke Lalonde
- Dept. of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign
| | - Danielle Baietto
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign
| | - Mayandi Sivaguru
- Carle Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign
| | - Rohit Bhargava
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign
| | - M Taher A Saif
- Dept. of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign
- Corresponding author: M Taher A Saif, Gutgsell Professor, Associate Head for Graduate Programs and Research, Mechanical Science and Engineering, Research Professor, Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, 2101D Mechanical Engineering Laboratory, 105 S. Mathews Avenue, Urbana, IL 61801, USA, , Tel: 217-333-8552, Fax: 217-244-6534, http://saif.mechse.illinois.edu/
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7
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Mimori-Kiyosue Y. Imaging mitotic processes in three dimensions with lattice light-sheet microscopy. Chromosome Res 2021; 29:37-50. [PMID: 33694045 PMCID: PMC8058003 DOI: 10.1007/s10577-021-09656-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022]
Abstract
There are few technologies that can capture mitotic processes occurring in three-dimensional space with the desired spatiotemporal resolution. Due to such technical limitations, our understanding of mitosis, which has been studied since the early 1880s, is still incomplete with regard to mitotic processes and their regulatory mechanisms at a molecular level. A recently developed high-resolution type of light-sheet microscopy, lattice light-sheet microscopy (LLSM), has achieved unprecedented spatiotemporal resolution scans of intracellular spaces at the whole-cell level. This technology enables experiments that were not possible before (e.g., tracking of growth of every spindle microtubule end and discrimination of individual chromosomes in living cells), thus providing a new avenue for the analysis of mitotic processes. Herein, principles of LLSM technology are introduced, as well as experimental techniques that became possible with LLSM. In addition, issues remaining to be solved for use of this technology in mitosis research, big image data problems, are presented to help guide mitosis research into a new era.
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Affiliation(s)
- Yuko Mimori-Kiyosue
- Laboratory for Molecular and Cellular Dynamics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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8
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Klymchenko AS, Liu F, Collot M, Anton N. Dye-Loaded Nanoemulsions: Biomimetic Fluorescent Nanocarriers for Bioimaging and Nanomedicine. Adv Healthc Mater 2021; 10:e2001289. [PMID: 33052037 DOI: 10.1002/adhm.202001289] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Indexed: 12/16/2022]
Abstract
Lipid nanoemulsions (NEs), owing to their controllable size (20 to 500 nm), stability and biocompatibility, are now frequently used in various fields, such as food, cosmetics, pharmaceuticals, drug delivery, and even as nanoreactors for chemical synthesis. Moreover, being composed of components generally recognized as safe (GRAS), they can be considered as "green" nanoparticles that mimic closely lipoproteins and intracellular lipid droplets. Therefore, they attracted attention as carriers of drugs and fluorescent dyes for both bioimaging and studying the fate of nanoemulsions in cells and small animals. In this review, the composition of dye-loaded NEs, methods for their preparation, and emerging biological applications are described. The design of bright fluorescent NEs with high dye loading and minimal aggregation-caused quenching (ACQ) is focused on. Common issues including dye leakage and NEs stability are discussed, highlighting advanced techniques for their characterization, such as Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS). Attempts to functionalize NEs surface are also discussed. Thereafter, biological applications for bioimaging and single-particle tracking in cells and small animals as well as biomedical applications for photodynamic therapy are described. Finally, challenges and future perspectives of fluorescent NEs are discussed.
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Affiliation(s)
- Andrey S. Klymchenko
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
| | - Fei Liu
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
- Université de Strasbourg CNRS CAMB UMR 7199 Strasbourg F‐67000 France
| | - Mayeul Collot
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
| | - Nicolas Anton
- Université de Strasbourg CNRS CAMB UMR 7199 Strasbourg F‐67000 France
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Dutta S, Rühle J, Schikora M, Deussner-Helfmann N, Heilemann M, Zatsepin T, Duchstein P, Zahn D, Knör G, Mokhir A. Red light-triggered photoreduction on a nucleic acid template. Chem Commun (Camb) 2020; 56:10026-10029. [PMID: 32728684 DOI: 10.1039/d0cc03086d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Conjugate Sn(iv)(pyropheophorbide a)dichloride-(peptide nucleic acid) catalyzes reduction of azobenzene derivatives in the presence of complementary nucleic acid (NA) upon irridiation with red light (660 nm). This is the first red light-induced NA-templated photoreduction. It is highly sensitive to single mismatches in the NA-template and can detect down to 5 nM NAs.
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Affiliation(s)
- Subrata Dutta
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany.
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10
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Zozulia O, Bachmann T, Mokhir A. Red Light Triggered Fluorogenic Reaction with Picomolar Sensitivity Toward Nucleic Acids. Bioconjug Chem 2019; 30:2023-2031. [PMID: 31195795 DOI: 10.1021/acs.bioconjchem.9b00299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We have previously reported on a red light triggered, singlet oxygen-mediated fluorogenic reaction that is templated in a highly sequence specific fashion by nucleic acids (S. Dutta, A. Fulop, A. Mokhir, Bioconjgate Chem. 2013, 24 (9), 1533-1542). Up to the present date, it has remained a single templated reaction responsive to nontoxic >650 nm light. However, it is operative only in the presence of relatively high (>2 nM) concentrations of templates that dramatically limit its applicability in nucleic acid detection. In the current work, we established that an inefficient intermolecular electron transfer involved in reduction of the 1,4-endoperoxide intermediate, formed in the rate-limiting reaction step, is responsible for inhibition of the reaction at low reagent concentrations. We suggested the solution of the problem which includes a combination of a cleavable (9-alkoxyanthracene) moiety with a two-electron donating fragment in one molecule. This approach enables the efficient intramolecular electron transfer to the endoperoxide intermediate in the critical reaction step. Due to the intramolecular character of the latter process, it is practically independent of concentration of the reagents. The reaction based on the improved cleavable moiety was found to be >200-fold more sensitive than the previously reported one. It is fast, sequence specific, and compatible with live cells. Accounting for short reactions times (<30 min), nontoxic trigger (red light), excellent sensitivity, and sequence specificity, this is presently the best reported photochemical templated reaction compatible with live cells.
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Affiliation(s)
- Oleksii Zozulia
- Friedrich-Alexander University Erlangen-Nürnberg (FAU) , Department of Chemistry and Pharmacy, Organic Chemistry Chair II , Nikolaus-Fiebiger-Strasse 10 , 91058 Erlangen , Germany
| | - Tobias Bachmann
- Friedrich-Alexander University Erlangen-Nürnberg (FAU) , Department of Chemistry and Pharmacy, Organic Chemistry Chair II , Nikolaus-Fiebiger-Strasse 10 , 91058 Erlangen , Germany
| | - Andriy Mokhir
- Friedrich-Alexander University Erlangen-Nürnberg (FAU) , Department of Chemistry and Pharmacy, Organic Chemistry Chair II , Nikolaus-Fiebiger-Strasse 10 , 91058 Erlangen , Germany
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11
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Nikolić M, Scarcelli G. Long-term Brillouin imaging of live cells with reduced absorption-mediated damage at 660 nm wavelength. BIOMEDICAL OPTICS EXPRESS 2019; 10:1567-1580. [PMID: 31086695 PMCID: PMC6484981 DOI: 10.1364/boe.10.001567] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 05/18/2023]
Abstract
In Brillouin microscopy, absorption-induced photodamage of incident light is the primary limitation on signal-to-noise ratio in many practical scenarios. Here we show that 660 nm may represent an optimal wavelength for Brillouin microscopy as it offers minimal absorption-mediated photodamage at high Brillouin scattering efficiency and the possibility to use a pure and narrow laser line from solid-state lasing medium. We demonstrate that live cells are ~80 times less susceptible to the 660 nm incident light compared to 532 nm light, which overall allows Brillouin imaging of up to more than 30 times higher SNR. We show that this improvement enables Brillouin imaging of live biological samples with improved accuracy, higher speed and/or larger fields of views with denser sampling.
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Affiliation(s)
- Miloš Nikolić
- Maryland Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Giuliano Scarcelli
- Maryland Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
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12
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Szydlowski NA, Go JS, Hu YS. Chromatin imaging and new technologies for imaging the nucleome. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1442. [PMID: 30456928 DOI: 10.1002/wsbm.1442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/03/2018] [Accepted: 10/16/2018] [Indexed: 12/15/2022]
Abstract
Synergistic developments in advanced fluorescent imaging and labeling techniques enable direct visualization of the chromatin structure and dynamics at the nanoscale level and in live cells. Super-resolution imaging encompasses a class of constantly evolving techniques that break the diffraction limit of fluorescence microscopy. Structured illumination microscopy provides a twofold resolution improvement and can readily achieve live multicolor imaging using conventional fluorophores. Single-molecule localization microscopy increases the spatial resolution by approximately 10-fold at the expense of slower acquisition speed. Stimulated emission-depletion microscopy generates a roughly fivefold resolution improvement with an imaging speed proportional to the scanning area. In parallel, advanced labeling strategies have been developed to "light up" global and sequence-specific DNA regions. DNA binding dyes have been exploited to achieve high labeling densities in single-molecule localization microscopy and enhance contrast in correlated light and electron microscopy. New-generation Oligopaint utilizes bioinformatics analyses to optimize the design of fluorescence in situ hybridization probes. Through sequential and combinatorial labeling, direct characterization of the DNA domain volume and length as well as the spatial organization of distinct topologically associated domains has been reported. In live cells, locus-specific labeling has been achieved by either inserting artificial loci next to the gene of interest, such as the repressor-operator array systems, or utilizing genome editing tools, including zinc finer proteins, transcription activator-like effectors, and the clustered regularly interspaced short palindromic repeats systems. Combined with single-molecule tracking, these labeling techniques enable direct visualization of intra- and inter-chromatin interactions. This article is categorized under: Laboratory Methods and Technologies > Imaging.
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Affiliation(s)
- Nicole A Szydlowski
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Jane S Go
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Ying S Hu
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
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13
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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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14
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Icha J, Weber M, Waters JC, Norden C. Phototoxicity in live fluorescence microscopy, and how to avoid it. Bioessays 2017; 39. [DOI: 10.1002/bies.201700003] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jaroslav Icha
- Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany
| | - Michael Weber
- Department of Cell Biology; Harvard Medical School; Boston MA USA
| | | | - Caren Norden
- Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany
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15
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Rashidfarrokhi A, Richina V, Tafesse FG. Visualizing the Early Stages of Phagocytosis. J Vis Exp 2017. [PMID: 28191879 DOI: 10.3791/54646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The mammalian body is equipped with various layers of mechanisms that help to defend itself from pathogen invasions. Professional phagocytes of the immune system - such as neutrophils, dendritic cells, and macrophages - retain the innate ability to detect and clear such invading pathogens through phagocytosis1. Phagocytosis involves choreographed events of membrane reorganization and actin remodeling at the cell surface2,3. Phagocytes successfully internalize and eradicate foreign molecules only when all stages of phagocytosis are fulfilled. These steps include recognition and binding of the pathogen by pattern recognition receptors (PRRs) residing at the cell surface, formation of phagocytic cup through actin-enriched membranous protrusions (pseudopods) to surround the particulate, and scission of the phagosome followed by phagolysosome maturation that results in the killing of the pathogen3,4. Imaging and quantification of various stages of phagocytosis is instrumental for elucidating the molecular mechanisms of this cellular process. The present manuscript reports methods to study the different phases of phagocytosis. We describe a microscope-based approach to visualize and quantify the binding, phagocytic cup formation, and the internalization of particulate by phagocytes. As phagocytosis occurs when innate receptors on phagocytic cells encounter ligands on a target particle bigger than 0.5 µm, the assays we present here comprise the use of pathogenic fungi Candida albicans and other particulates such as zymosan and IgG-coated beads.
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Affiliation(s)
| | | | - Fikadu G Tafesse
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Ragon Institute of MGH, MIT and Harvard;
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16
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The Effect of Surface Charges on the Cellular Uptake of Liposomes Investigated by Live Cell Imaging. Pharm Res 2017; 34:704-717. [DOI: 10.1007/s11095-017-2097-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/04/2017] [Indexed: 12/22/2022]
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17
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Abstract
AbstractLive-cell and live-tissue imaging using fluorescence optical microscopes presents an inherent trade-off between image quality and photodamage. Spatially-controlled illumination microscopy (SCIM) aims to strike the right balance between obtaining good image quality and minimizing the risk of photodamage. In traditional imaging, illumination is performed with a spatially-uniform light dose resulting in spatially-variable detected signals. SCIM adopts an alternative imaging approach where illumination is performed with a spatially-variable light dose resulting in spatially-uniform detected signals. The actual image information of the biological specimen in SCIM is predominantly encoded in the illumination profile. SCIM uses real-time spatial control of illumination in the imaging of fluorescent biological specimens. This alternative imaging paradigm reduces the overall illumination light dose during imaging, which facilitates prolonged imaging of live biological specimens by minimizing photodamage without compromising image quality. Additionally, the dynamic range of a SCIM image is no longer limited by the dynamic range of the detector (or camera), since it employs a uniform detection strategy. The large dynamic range of SCIM is predominantly determined by the illumination profile, and is advantageous for imaging both live and fixed biological specimens. In the present review, the concept and working mechanisms of SCIM are discussed, together with its application in various types of optical microscopes.
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18
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Contractile dynamics change before morphological cues during fluorescence [corrected] illumination. Sci Rep 2015; 5:18513. [PMID: 26691776 PMCID: PMC4686977 DOI: 10.1038/srep18513] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/19/2015] [Indexed: 01/15/2023] Open
Abstract
Illumination can have adverse effects on live cells. However, many experiments, e.g. traction force microscopy, rely on fluorescence microscopy. Current methods to assess undesired photo-induced cell changes rely on qualitative observation of changes in cell morphology. Here we utilize a quantitative technique to identify the effect of light on cell contractility prior to morphological changes. Fibroblasts were cultured on soft elastic hydrogels embedded with fluorescent beads. The adherent cells generated contractile forces that deform the substrate. Beads were used as fiducial markers to quantify the substrate deformation over time, which serves as a measure of cell force dynamics. We find that cells exposed to moderate fluorescence illumination (λ = 540–585 nm, I = 12.5 W/m2, duration = 60 s) exhibit rapid force relaxation. Strikingly, cells exhibit force relaxation after only 2 s of exposure, suggesting that photo-induced relaxation occurs nearly immediately. Evidence of photo-induced morphological changes were not observed for 15–30 min after illumination. Force relaxation and morphological changes were found to depend on wavelength and intensity of excitation light. This study demonstrates that changes in cell contractility reveal evidence of a photo-induced cell response long before any morphological cues.
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19
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Light-induced cell damage in live-cell super-resolution microscopy. Sci Rep 2015; 5:15348. [PMID: 26481189 PMCID: PMC4611486 DOI: 10.1038/srep15348] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/22/2015] [Indexed: 12/11/2022] Open
Abstract
Super-resolution microscopy can unravel previously hidden details of cellular structures but requires high irradiation intensities to use the limited photon budget efficiently. Such high photon densities are likely to induce cellular damage in live-cell experiments. We applied single-molecule localization microscopy conditions and tested the influence of irradiation intensity, illumination-mode, wavelength, light-dose, temperature and fluorescence labeling on the survival probability of different cell lines 20–24 hours after irradiation. In addition, we measured the microtubule growth speed after irradiation. The photo-sensitivity is dramatically increased at lower irradiation wavelength. We observed fixation, plasma membrane permeabilization and cytoskeleton destruction upon irradiation with shorter wavelengths. While cells stand light intensities of ~1 kW cm−2 at 640 nm for several minutes, the maximum dose at 405 nm is only ~50 J cm−2, emphasizing red fluorophores for live-cell localization microscopy. We also present strategies to minimize phototoxic factors and maximize the cells ability to cope with higher irradiation intensities.
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20
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Kim DNH, Teitell MA, Reed J, Zangle TA. Hybrid random walk-linear discriminant analysis method for unwrapping quantitative phase microscopy images of biological samples. JOURNAL OF BIOMEDICAL OPTICS 2015; 20:111211. [PMID: 26305212 PMCID: PMC4652035 DOI: 10.1117/1.jbo.20.11.111211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/22/2015] [Indexed: 05/30/2023]
Abstract
Standard algorithms for phase unwrapping often fail for interferometric quantitative phase imaging (QPI) of biological samples due to the variable morphology of these samples and the requirement to image at low light intensities to avoid phototoxicity. We describe a new algorithm combining random walk-based image segmentation with linear discriminant analysis (LDA)-based feature detection, using assumptions about the morphology of biological samples to account for phase ambiguities when standard methods have failed. We present three versions of our method: first, a method for LDA image segmentation based on a manually compiled training dataset; second, a method using a random walker (RW) algorithm informed by the assumed properties of a biological phase image; and third, an algorithm which combines LDA-based edge detection with an efficient RW algorithm. We show that the combination of LDA plus the RW algorithm gives the best overall performance with little speed penalty compared to LDA alone, and that this algorithm can be further optimized using a genetic algorithm to yield superior performance for phase unwrapping of QPI data from biological samples.
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Affiliation(s)
- Diane N. H. Kim
- University of California, Los Angeles, Department of Bioengineering, TLSB 3126, California 90095, United States
| | - Michael A. Teitell
- University of California, Los Angeles, Department of Bioengineering, TLSB 3126, California 90095, United States
- University of California, Los Angeles, Jonsson Comprehensive Cancer Center, 8-950 Factor Building, California 90095, United States
- University of California, Los Angeles, Broad Stem Cell Research Center, Box 957357, California 90095, United States
- University of California, Los Angeles, David Geffen School of Medicine, Department of Pathology and Laboratory Medicine, MRL 4762, California 90095, United States
- University of California, Los Angeles, NanoSystems Institute, 570 Westwood Plaza, California 90095, United States
- University of California, Los Angeles, Molecular Biology Institute, Box 951570, California 90095, United States
| | - Jason Reed
- Virginia Commonwealth University, Department of Physics, 701 West Grace Street, Richmond, Virginia 23284, United States
- Virginia Commonwealth University, Massey Cancer Center, 401 College Street, Richmond, Virginia 23284, United States
| | - Thomas A. Zangle
- University of California, Los Angeles, Department of Bioengineering, TLSB 3126, California 90095, United States
- University of California, Los Angeles, Jonsson Comprehensive Cancer Center, 8-950 Factor Building, California 90095, United States
- University of California, Los Angeles, Broad Stem Cell Research Center, Box 957357, California 90095, United States
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21
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Zangle TA, Teitell MA. Live-cell mass profiling: an emerging approach in quantitative biophysics. Nat Methods 2014; 11:1221-8. [PMID: 25423019 PMCID: PMC4319180 DOI: 10.1038/nmeth.3175] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 07/22/2014] [Indexed: 12/16/2022]
Abstract
Cell mass, volume and growth rate are tightly controlled biophysical parameters in cellular development and homeostasis, and pathological cell growth defines cancer in metazoans. The first measurements of cell mass were made in the 1950s, but only recently have advances in computer science and microfabrication spurred the rapid development of precision mass-quantifying approaches. Here we discuss available techniques for quantifying the mass of single live cells with an emphasis on relative features, capabilities and drawbacks for different applications.
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Affiliation(s)
- Thomas A Zangle
- Department of Bioengineering, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Michael A Teitell
- 1] Department of Bioengineering, University of California, Los Angeles (UCLA), Los Angeles, California, USA. [2] Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA. [3] California NanoSystems Institute, UCLA, Los Angeles, California, USA. [4] Broad Stem Cell Research Center, UCLA, Los Angeles, California, USA. [5] Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA. [6] Molecular Biology Institute, UCLA, Los Angeles, California, USA
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22
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Chen BC, Legant WR, Wang K, Shao L, Milkie DE, Davidson MW, Janetopoulos C, Wu XS, Hammer JA, Liu Z, English BP, Mimori-Kiyosue Y, Romero DP, Ritter AT, Lippincott-Schwartz J, Fritz-Laylin L, Mullins RD, Mitchell DM, Bembenek JN, Reymann AC, Böhme R, Grill SW, Wang JT, Seydoux G, Tulu US, Kiehart DP, Betzig E. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 2014; 346:1257998. [PMID: 25342811 DOI: 10.1126/science.1257998] [Citation(s) in RCA: 1135] [Impact Index Per Article: 113.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Although fluorescence microscopy provides a crucial window into the physiology of living specimens, many biological processes are too fragile, are too small, or occur too rapidly to see clearly with existing tools. We crafted ultrathin light sheets from two-dimensional optical lattices that allowed us to image three-dimensional (3D) dynamics for hundreds of volumes, often at subsecond intervals, at the diffraction limit and beyond. We applied this to systems spanning four orders of magnitude in space and time, including the diffusion of single transcription factor molecules in stem cell spheroids, the dynamic instability of mitotic microtubules, the immunological synapse, neutrophil motility in a 3D matrix, and embryogenesis in Caenorhabditis elegans and Drosophila melanogaster. The results provide a visceral reminder of the beauty and the complexity of living systems.
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Affiliation(s)
- Bi-Chang Chen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Wesley R Legant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kai Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Lin Shao
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Daniel E Milkie
- Coleman Technologies, Incorporated, Newtown Square, PA 19073, USA
| | - Michael W Davidson
- National High Magnetic Field Laboratory and Department of Biological Science, Florida State University, Tallahassee, FL 32310, USA
| | - Chris Janetopoulos
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA 19104, USA
| | - Xufeng S Wu
- Laboratory of Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John A Hammer
- Laboratory of Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Brian P English
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Yuko Mimori-Kiyosue
- Optical Image Analysis Unit, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Daniel P Romero
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alex T Ritter
- Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA. Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge CB2 0XY, England, UK
| | - Jennifer Lippincott-Schwartz
- Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lillian Fritz-Laylin
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - R Dyche Mullins
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Diana M Mitchell
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Joshua N Bembenek
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Anne-Cecile Reymann
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany. Max Planck Institute for the Physics of Complex Systems, 01307 Dresden, Germany
| | - Ralph Böhme
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany. Max Planck Institute for the Physics of Complex Systems, 01307 Dresden, Germany
| | - Stephan W Grill
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany. Max Planck Institute for the Physics of Complex Systems, 01307 Dresden, Germany
| | - Jennifer T Wang
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - U Serdar Tulu
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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23
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Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens. Cell 2013; 151:1370-85. [PMID: 23217717 PMCID: PMC3615549 DOI: 10.1016/j.cell.2012.10.008] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 06/20/2012] [Accepted: 10/01/2012] [Indexed: 11/22/2022]
Abstract
Optical imaging of the dynamics of living specimens involves tradeoffs between spatial resolution, temporal resolution, and phototoxicity, made more difficult in three dimensions. Here, however, we report that rapid three-dimensional (3D) dynamics can be studied beyond the diffraction limit in thick or densely fluorescent living specimens over many time points by combining ultrathin planar illumination produced by scanned Bessel beams with super-resolution structured illumination microscopy. We demonstrate in vivo karyotyping of chromosomes during mitosis and identify different dynamics for the actin cytoskeleton at the dorsal and ventral surfaces of fibroblasts. Compared to spinning disk confocal microscopy, we demonstrate substantially reduced photodamage when imaging rapid morphological changes in D. discoideum cells, as well as improved contrast and resolution at depth within developing C. elegans embryos. Bessel beam structured plane illumination thus promises new insights into complex biological phenomena that require 4D subcellular spatiotemporal detail in either a single or multicellular context.
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24
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Jensen EC. Overview of Live-Cell Imaging: Requirements and Methods Used. Anat Rec (Hoboken) 2012; 296:1-8. [DOI: 10.1002/ar.22554] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 06/05/2012] [Accepted: 07/26/2012] [Indexed: 11/11/2022]
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25
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Schilling Z, Frank E, Magidson V, Wason J, Lončarek J, Boyer K, Wen J, Khodjakov A. Predictive-focus illumination for reducing photodamage in live-cell microscopy. J Microsc 2012; 246:160-7. [PMID: 22429382 PMCID: PMC3582196 DOI: 10.1111/j.1365-2818.2012.03605.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Due to photobleaching and phototoxicity induced by high-intensity excitation light, the number of fluorescence images that can be obtained in live cells is always limited. This limitation becomes particularly prominent in multidimensional recordings when multiple Z-planes are captured at every time point. Here we present a simple technique, termed predictive-focus illumination (PFI), which helps to minimize cells' exposure to light by decreasing the number of Z-planes that need to be captured in live-cell 3D time-lapse recordings. PFI utilizes computer tracking to predict positions of objects of interest (OOIs) and restricts image acquisition to small dynamic Z-regions centred on each OOI. Importantly, PFI does not require hardware modifications and it can be easily implemented on standard wide-field and spinning-disc confocal microscopes.
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Affiliation(s)
- Z. Schilling
- Department of Electrical, Computer, and Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - E. Frank
- Department of Electrical, Computer, and Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - V. Magidson
- Department of Mechanical, Aerospace, and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - J. Wason
- Department of Electrical, Computer, and Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - J. Lončarek
- Wadsworth Center, NY State Dept. of Health, Albany, NY, USA
| | - K. Boyer
- Department of Electrical, Computer, and Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - J. Wen
- Department of Electrical, Computer, and Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
- Department of Mechanical, Aerospace, and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - A. Khodjakov
- Wadsworth Center, NY State Dept. of Health, Albany, NY, USA
- Department of Biology, Rensselaer Polytechnic Institute, Troy, NY, USA
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26
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van de Linde S, Heilemann M, Sauer M. Live-cell super-resolution imaging with synthetic fluorophores. Annu Rev Phys Chem 2012; 63:519-40. [PMID: 22404589 DOI: 10.1146/annurev-physchem-032811-112012] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Super-resolution imaging methods now can provide spatial resolution that is well below the diffraction limit approaching virtually molecular resolution. They can be applied to biological samples and provide new and exciting views on the structural organization of cells and the dynamics of biomolecular assemblies on wide timescales. These revolutionary developments come with novel requirements for fluorescent probes, labeling techniques, and data interpretation strategies. Synthetic fluorophores have a small size, are available in many colors spanning the whole spectrum, and can easily be chemically modified and used for stoichiometric labeling of proteins in live cells. Because of their brightness, their photostability, and their ability to be operated as photoswitchable fluorophores even in living cells under physiological conditions, synthetic fluorophores have the potential to substantially accelerate the broad application of live-cell super-resolution imaging methods.
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Affiliation(s)
- Sebastian van de Linde
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Germany
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27
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Huang Y, Hou H, Yi Q, Zhang Y, Chen D, Jiang E, Xia Y, Fenech M, Shi Q. The fate of micronucleated cells post X-irradiation detected by live cell imaging. DNA Repair (Amst) 2011; 10:629-38. [DOI: 10.1016/j.dnarep.2011.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 03/30/2011] [Accepted: 04/05/2011] [Indexed: 10/18/2022]
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28
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Lee K, Kenny AE, Rieder CL. Caspase activity is not required for the mitotic checkpoint or mitotic slippage in human cells. Mol Biol Cell 2011; 22:2470-9. [PMID: 21613548 PMCID: PMC3135473 DOI: 10.1091/mbc.e11-03-0228] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Biochemical studies suggest that caspase activity is required for a functional mitotic checkpoint (MC) and mitotic slippage. To test this directly, we followed nontransformed human telomerase immortalized human retinal pigment epithelia (RPE-1) cells through mitosis after inhibiting or depleting selected caspases. We found that inhibiting caspases individually, in combination, or in toto did not affect the duration or fidelity of mitosis in otherwise untreated cells. When satisfaction of the MC was prevented with 500 nM nocodazole or 2.5 μM dimethylenastron (an Eg5 inhibitor), 92-100% of RPE-1 cells slipped from mitosis in the presence of pan-caspase inhibitors or after simultaneously depleting caspase-3 and -9, and they did so with the same kinetics (~21-22 h) as after treatment with nocodazole or Eg5 inhibitors alone. Surprisingly, inhibiting or depleting caspase-9 alone doubled the number of nocodazole-treated, but not Eg5-inhibited, cells that died in mitosis. In addition, inhibiting or depleting caspase-9 and -3 together accelerated the rate of slippage ~40% (to ~13-15 h). Finally, nocodazole-treated cells that recently slipped through mitosis in the presence or absence of pan-caspase inhibitors contained numerous BubR1 foci in their nuclei. From these data, we conclude that caspase activity is not required for a functional MC or for mitotic slippage.
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Affiliation(s)
- Kyunghee Lee
- Division of Translational Medicine, Biggs Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA
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29
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Abstract
Although micronuclei (MNi) have been extensively used to evaluate genotoxic effects and chromosome instability, the most basic issue regarding their formation was not completely addressed until recently, due to limitations of traditional experimental methods. The development of live-cell imaging, combined with genetically engineered chromosome labelling techniques makes it possible to investigate the origin of a micronucleus in a single cell in a real-time and high-throughput manner. Here, we review all the available studies on the origins of MNi in live cells and discuss novel findings based on this recently emerged methodology. Some unsolved questions on MNi formation and limitations of live-cell imaging in the investigation of MNi have also been discussed.
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Affiliation(s)
- Yun Huang
- Laboratory of Molecular and Cell Genetics, Department of Biochemistry and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, PR China
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30
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Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. Nat Methods 2011; 8:417-23. [PMID: 21378978 DOI: 10.1038/nmeth.1586] [Citation(s) in RCA: 592] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 02/27/2011] [Indexed: 12/27/2022]
Abstract
A key challenge when imaging living cells is how to noninvasively extract the most spatiotemporal information possible. Unlike popular wide-field and confocal methods, plane-illumination microscopy limits excitation to the information-rich vicinity of the focal plane, providing effective optical sectioning and high speed while minimizing out-of-focus background and premature photobleaching. Here we used scanned Bessel beams in conjunction with structured illumination and/or two-photon excitation to create thinner light sheets (<0.5 μm) better suited to three-dimensional (3D) subcellular imaging. As demonstrated by imaging the dynamics of mitochondria, filopodia, membrane ruffles, intracellular vesicles and mitotic chromosomes in live cells, the microscope currently offers 3D isotropic resolution down to ∼0.3 μm, speeds up to nearly 200 image planes per second and the ability to noninvasively acquire hundreds of 3D data volumes from single living cells encompassing tens of thousands of image frames.
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31
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Kinnally KW, Martinez-Caballero S, Dejean LM. Detection of the mitochondrial apoptosis-induced channel (MAC) and its regulation by Bcl-2 family proteins. ACTA ACUST UNITED AC 2011; Chapter 2:Unit2.12. [PMID: 20941703 DOI: 10.1002/0471140856.tx0212s30] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Apoptosis is a phenomenon fundamental to higher eukaryotes that is integral to such diverse cellular processes as tissue homeostasis, organogenesis, and response to toxins. The release from mitochondria of apoptotic factors such as cytochrome c is a key step during apoptosis of most cells. Cytochrome c release occurs through the MAC (mitochondrial apoptosis-induced channel), a pore which forms in the mitochondrial outer membrane during early apoptosis and is exquisitely regulated by the Bcl-2 family of proteins. This unit presents basic and advanced tools for detecting MAC and defining its regulation by Bcl-2 family proteins and pharmacological agents. Protocols include the use of time-lapse video-microscopy to monitor the onset of apoptosis in living cells and patch-clamp techniques for mitochondria or proteoliposomes containing mitochondrial proteins, which allow direct detection of MAC. These approaches enable an evaluation of the role of MAC and mitochondria in apoptosis of a variety of cell types by many inducers.
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32
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Abstract
Since the first schematic illustrations of dividing cells, we have come a long way in characterising eukaryotic cells and defining their cell-cycle status thanks to a number of complementary approaches. Although most of these approaches rely on cell-fixation procedures to identify molecular components in cell lysates, cultured cells or tissues, the development of GFP technology has enabled visualisation of virtually any fusion protein in cellulo and in vivo, and the exploitation of functional elements with well-defined spatiotemporal characteristics has enabled the development of genetically encoded fluorescent markers of cell-cycle phases, thus providing novel means of characterising the status of living cells in real time with high resolution. Together with technological advances in fluorescence chemistry and imaging approaches, the more recent development of fluorescent biosensors has provided direct means of probing cell-cycle regulators and of studying their dynamics with high spatial and temporal resolution. Here we review classical approaches that rely on cell fixation to characterise the cell-cycle status and its regulatory enzymes, and we describe the more recent development of cell-cycle markers based on genetically encoded fusions of fluorescent proteins with characteristic cell-cycle features, and of fluorescent biosensor technology to probe cell-cycle regulators in living cells. Biosensors not only provide a means of characterising the behaviour of cell-cycle regulators in their natural environment, they are also very useful for comparative studies of biological processes in healthy and pathological conditions, and can be further applied to diagnostic approaches to assess the status of a specific target, and to monitor response to therapeutic intervention.
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33
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Abstract
Changes in cellular organization and chromosome dynamics that occur during mitosis are tightly coordinated to ensure accurate inheritance of genomic and cellular content. Hallmark events of mitosis, such as chromosome movement, can be readily tracked on an individual cell basis using time-lapse fluorescence microscopy of mammalian cell lines expressing specific GFP-tagged proteins. In combination with RNAi-based depletion, this can be a powerful method for pinpointing the stage(s) of mitosis where defects occur after levels of a particular protein have been lowered. In this protocol, we present a basic method for assessing the effect of depleting a potential mitotic regulatory protein on the timing of mitosis. Cells are transfected with siRNA, placed in a stage-top incubation chamber, and imaged using an automated fluorescence microscope. We describe how to use software to set up a time-lapse experiment, how to process the image sequences to make either still-image montages or movies, and how to quantify and analyze the timing of mitotic stages using a cell-line expressing mCherry-tagged histone H2B. Finally, we discuss important considerations for designing a time-lapse experiment. This strategy is complementary to other approaches and offers the advantages of 1) sensitivity to changes in kinetics that might not be observed when looking at cells as a population and 2) analysis of mitosis without the need to synchronize the cell cycle using drug treatments. The visual information from such imaging experiments not only allows the sub-stages of mitosis to be assessed, but can also provide unexpected insight that would not be apparent from cell cycle analysis by FACS.
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Affiliation(s)
- Douglas R Mackay
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, USA.
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Lee K, Kenny AE, Rieder CL. P38 mitogen-activated protein kinase activity is required during mitosis for timely satisfaction of the mitotic checkpoint but not for the fidelity of chromosome segregation. Mol Biol Cell 2010; 21:2150-60. [PMID: 20462950 PMCID: PMC2893980 DOI: 10.1091/mbc.e10-02-0125] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We find that in the absence of p38 activity, human cells form longer spindles on which mitotic checkpoint satisfaction is transiently delayed. However, the cells ultimately divide normally. We conclude that normal p38 activity is required for the timely attachment of kinetochores to the spindle, but not for the fidelity of mitosis. Although p38 activity is reported to be required as cells enter mitosis for proper spindle assembly and checkpoint function, its role during the division process remains controversial in lieu of direct data. We therefore conducted live cell studies to determine the effect on mitosis of inhibiting or depleting p38. We found that in the absence of p38 activity the duration of mitosis is prolonged by ∼40% in nontransformed human RPE-1, ∼80% in PtK2 (rat kangaroo), and ∼25% in mouse cells, and this prolongation leads to an elevated mitotic index. However, under this condition chromatid segregation and cytokinesis are normal. Using Mad2/YFP-expressing cells, we show the prolongation of mitosis in the absence of p38 activity is directly due to a delay in satisfying the mitotic checkpoint. Inhibiting p38 did not affect the rate of chromosome motion; however, it did lead to the formation of significantly (10%) longer metaphase spindles. From these data we conclude that normal p38 activity is required for the timely stable attachment of all kinetochores to spindle microtubules, but not for the fidelity of the mitotic process. We speculate that p38 activity promotes timely checkpoint satisfaction by indirectly influencing those motor proteins (e.g., Klp10, Klp67A) involved in regulating the dynamics of kinetochore microtubule ends.
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Affiliation(s)
- Kyunghee Lee
- Division of Translational Medicine, Wadsworth Center, Albany, NY 12201-0509, USA
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35
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Mavrakis M, Pourquié O, Lecuit T. Lighting up developmental mechanisms: how fluorescence imaging heralded a new era. Development 2010; 137:373-87. [DOI: 10.1242/dev.031690] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Embryology and genetics have given rise to a mechanistic framework that explains the architecture of a developing organism. Until recently, however, such studies suffered from a lack of quantification and real-time visualization at the subcellular level, limiting their ability to monitor the dynamics of developmental processes. Live imaging using fluorescent proteins has overcome these limitations, uncovering unprecedented insights that call many established models into question. We review how the study of patterning, cell polarization and morphogenesis has benefited from this technology and discuss the possibilities offered by fluorescence imaging and by the contributions of quantitative disciplines.
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Affiliation(s)
- Manos Mavrakis
- IBDML (Institut de Biologie du Développement de Marseille Luminy), UMR6216 CNRS—Université de la Méditerranée, Parc Scientifique de Luminy BP 907, 13009 Marseille, France
| | - Olivier Pourquié
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) / Inserm U964 / CNRS UMR7104, 67400 Illkirch, France; and Université de Strasbourg, 67000 Strasbourg, France
| | - Thomas Lecuit
- IBDML (Institut de Biologie du Développement de Marseille Luminy), UMR6216 CNRS—Université de la Méditerranée, Parc Scientifique de Luminy BP 907, 13009 Marseille, France
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36
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Law GL, Man C, Parker D, Walton JW. Observation of the selective staining of chromosomal DNA in dividing cells using a luminescent terbium(iii) complex. Chem Commun (Camb) 2010; 46:2391-3. [DOI: 10.1039/b924679g] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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37
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Walczak CE, Rizk RS, Shaw SL. The use of fluorescence redistribution after photobleaching for analysis of cellular microtubule dynamics. Methods Cell Biol 2010; 97:35-52. [PMID: 20719264 DOI: 10.1016/s0091-679x(10)97003-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Microtubules (MTs) are highly dynamic polymers that serve as tracks for vesicular movement during interphase and as structural components of the mitotic spindle, which is used to segregate the genetic material. MT dynamics are highly regulated wherein MTs turnover differentially between interphase and mitosis. Within the mitotic spindle, there are distinct classes of MTs with different dynamic properties. To understand how cellular proteins regulate the dynamics of MTs, it is necessary to have methods to assess their turnover properties. In this chapter we present approaches to assess MT dynamics in cultured mammalian cells using fluorescence redistribution after photobleaching. We include a discussion of cell culture and imaging conditions that maintain cell viability. We also provide an extensive discussion of both data collection and analysis that are utilized to estimate the turnover dynamics of MTs.
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Affiliation(s)
- Claire E Walczak
- Medical Sciences, Indiana University, Bloomington, Indiana 47405, USA
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38
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Robertson JB, Zhang Y, Johnson CH. Light-emitting diode flashlights as effective and inexpensive light sources for fluorescence microscopy. J Microsc 2009; 236:1-4. [PMID: 19772530 DOI: 10.1111/j.1365-2818.2009.03208.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Light-emitting diodes (LEDs) are becoming more commonly used as light sources for fluorescence microscopy. We describe the adaptation of a commercially available light-emitting diode flashlight for use as a source for fluorescence excitation. This light source is long-lived, inexpensive and is effective for excitation in the range of 440-600 nm.
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Affiliation(s)
- J B Robertson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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39
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Brito DA, Rieder CL. The ability to survive mitosis in the presence of microtubule poisons differs significantly between human nontransformed (RPE-1) and cancer (U2OS, HeLa) cells. ACTA ACUST UNITED AC 2009; 66:437-47. [PMID: 18792104 DOI: 10.1002/cm.20316] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We used live cell imaging to compare the fate of human nontransformed (RPE-1) and cancer (HeLa, U2OS) cells as they entered mitosis in nocodazole or taxol. In the same field, and in either drug, a cell in all lines could die in mitosis, exit mitosis and die within 10 h, or exit mitosis and survive > or =10 h. Relative to RPE-1 cells, significantly fewer HeLa or U2OS cells survived mitosis or remained viable after mitosis: in nocodazole concentrations that inhibit spindle microtubule assembly, or in 500 nM taxol, 30% and 27% of RPE-1 cells, respectively, died in or within 10 h of exiting mitosis while 90% and 49% of U2OS and 78% and 81% of HeLa died. This was even true for clinically relevant taxol concentrations (5 nM) which killed 93% and 46%, respectively, of HeLa and U2OS cells in mitosis or within 10 h of escaping mitosis, compared to 1% of RPE-1 cells. Together these data imply that studies using HeLa or U2OS cells, harvested after a prolonged block in mitosis with nocodazole or taxol, are significantly contaminated with dead or dying cells. We also found that the relationship between the duration of mitosis and survival is drug and cell type specific and that lethality is related to the cell type and drug used to prevent satisfaction of the kinetochore attachment checkpoint. Finally, work with a pan-caspase inhibitor suggests that the primary apoptotic pathway triggered by nocodazole during mitosis in RPE-1 cells is not active in U2OS cells. Cell Motil. Cytoskeleton 2008. (c) 2008 Wiley-Liss, Inc.
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Affiliation(s)
- Daniela A Brito
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York, USA
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40
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Day RN, Davidson MW. The fluorescent protein palette: tools for cellular imaging. Chem Soc Rev 2009; 38:2887-921. [PMID: 19771335 DOI: 10.1039/b901966a] [Citation(s) in RCA: 559] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This critical review provides an overview of the continually expanding family of fluorescent proteins (FPs) that have become essential tools for studies of cell biology and physiology. Here, we describe the characteristics of the genetically encoded fluorescent markers that now span the visible spectrum from deep blue to deep red. We identify some of the novel FPs that have unusual characteristics that make them useful reporters of the dynamic behaviors of proteins inside cells, and describe how many different optical methods can be combined with the FPs to provide quantitative measurements in living systems (227 references).
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Affiliation(s)
- Richard N Day
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA.
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41
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Hahn AT, Jones JT, Meyer T. Quantitative analysis of cell cycle phase durations and PC12 differentiation using fluorescent biosensors. Cell Cycle 2009; 8:1044-52. [PMID: 19270522 DOI: 10.4161/cc.8.7.8042] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cell cycle analysis typically relies on fixed time-point measurements of cells in particular phases of the cell cycle. The cell cycle, however, is a dynamic process whose subtle shifts are lost by fixed time-point methods. Live-cell fluorescent biosensors and time-lapse microscopy allows the collection of temporal information about real time cell cycle progression and arrest. Using two genetically-encoded biosensors, we measured the precision of the G(1), S, G(2) and M cell cycle phase durations in different cell types and identified a bimodal G(1) phase duration in a fibroblast cell line that is not present in the other cell types. Using a cell line model for neuronal differentiation, we demonstrated that NGF-induced neurite extension occurs independently of NGF-induced cell cycle G(1) phase arrest. Thus, we have begun to use cell cycle fluorescent biosensors to examine the proliferation of cell populations at the resolution of individual cells and neuronal differentiation as a dynamic process of parallel cell cycle arrest and neurite outgrowth.
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Affiliation(s)
- Angela T Hahn
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
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42
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DiMaio MA, Mikhailov A, Rieder CL, Von Hoff DD, Palazzo RE. The small organic compound HMN-176 delays satisfaction of the spindle assembly checkpoint by inhibiting centrosome-dependent microtubule nucleation. Mol Cancer Ther 2009; 8:592-601. [PMID: 19258425 DOI: 10.1158/1535-7163.mct-08-0876] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
HMN-176 is a potential new cancer therapeutic known to retard the proliferation of tumor cell lines. Here, we show that this compound inhibits meiotic spindle assembly in surf clam oocytes and delays satisfaction of the spindle assembly checkpoint in human somatic cells by inducing the formation of short and/or multipolar spindles. HMN-176 does not affect centrosome assembly, nuclear envelope breakdown, or other aspects of meiotic or mitotic progression, nor does it affect the kinetics of Spisula or mammalian microtubule (MT) assembly in vitro. Notably, HMN-176 inhibits the formation of centrosome-nucleated MTs (i.e., asters) in Spisula oocytes and oocyte extracts, as well as from isolated Spisula or mammalian centrosomes in vitro. Together, these results reveal that HMN-176 is a first-in-class anticentrosome drug that inhibits proliferation, at least in part, by disrupting centrosome-mediated MT assembly during mitosis.
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Affiliation(s)
- Michael A DiMaio
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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43
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Stout JR, Rizk RS, Walczak CE. Protein inhibition by microinjection and RNA-mediated interference in tissue culture cells: complementary approaches to study protein function. Methods Mol Biol 2009; 518:77-97. [PMID: 19085130 PMCID: PMC2904950 DOI: 10.1007/978-1-59745-202-1_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A major goal in cell biology is to understand the molecular mechanisms of the biological process under study, which requires functional information about the roles of individual proteins in the cell. For many non-genetic model organisms researchers have relied on the use of inhibitory reagents, such as antibodies that can be microinjected into cells. More recently, the advent of RNA-mediated interference (RNAi) has allowed scientists to knockdown individual proteins and to examine the consequences of the knockdown. In this chapter we present a comparison between microinjection of inhibitory reagents and RNAi for the analysis of protein function in mammalian tissue culture cells, providing both a description of the techniques as well as a discussion of the benefits and drawbacks of each approach. In addition, we present a strategy to employ RNAi for organisms without a sequenced genome. While the focus of our research is on the organization of the mitotic spindle during cell division and thus the examples utilized are from that system, the approaches described here should be readily applicable to multiple experimental models.
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Affiliation(s)
- Jane R Stout
- Department of Biochemistry and Molecular Biology, Indiana University Medical Sciences, Bloomington, IN, USA
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44
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Abstract
The formation of a bipolar spindle is essential for the equal segregation of duplicated DNA into two daughter cells during mitosis. Spindle bipolarity is largely dependent on the mitotic cell possessing two centrosomes that can each establish one spindle pole. The centrosome is also now known to regulate many other aspects of cell cycle progression, including G1/S progression, spindle orientation and symmetry, cytokinesis, and checkpoint signalling. As a result, defects in centrosome arrangement or number can lead to loss of cell polarity, defective cell division, and abnormal chromosome segregation, all events that are typical of cancer cells. Indeed, cancer cells often exhibit overduplicated centrosomes and multipolar spindles. Here, we outline a number of fluorescence imaging methodologies that can be used to study events of the centrosome duplication cycle, as well as the dynamics of individual centrosome proteins. Specifically, we discuss the generation and imaging of cell lines with fluorescently labelled centrosomes, the use of photobleaching methods to measure the dynamics of centrosome proteins, and assays for observing centrosome overduplication and centrosome separation in fixed and live cells. These experimental approaches can provide important information on the regulation of centrosomes, their role in normal cell cycle progression and how their deregulation might contribute to the deleterious phenotypes of malignant cancer cells.
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45
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Brito DA, Yang Z, Rieder CL. Microtubules do not promote mitotic slippage when the spindle assembly checkpoint cannot be satisfied. ACTA ACUST UNITED AC 2008; 182:623-9. [PMID: 18710927 PMCID: PMC2518701 DOI: 10.1083/jcb.200805072] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
When the spindle assembly checkpoint (SAC) cannot be satisfied, cells exit mitosis via mitotic slippage. In microtubule (MT) poisons, slippage requires cyclin B proteolysis, and it appears to be accelerated in drug concentrations that allow some MT assembly. To determine if MTs accelerate slippage, we followed mitosis in human RPE-1 cells exposed to various spindle poisons. At 37°C, the duration of mitosis in nocodazole, colcemid, or vinblastine concentrations that inhibit MT assembly varied from 20 to 30 h, revealing that different MT poisons differentially depress the cyclin B destruction rate during slippage. The duration of mitosis in Eg5 inhibitors, which induce monopolar spindles without disrupting MT dynamics, was the same as in cells lacking MTs. Thus, in the presence of numerous unattached kinetochores, MTs do not accelerate slippage. Finally, compared with cells lacking MTs, exit from mitosis is accelerated over a range of spindle poison concentrations that allow MT assembly because the SAC becomes satisfied on abnormal spindles and not because slippage is accelerated.
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Affiliation(s)
- Daniela A Brito
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, NY 12222, USA
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46
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Abstract
Live-cell imaging is a powerful tool which allows the observation of dynamic cellular processes while maintaining the native organization of the cell. Its advantages over other methods that disrupt cell integrity are abundantly evident in the study of cell division, where multiple subcellular organelles and molecules are involved in dynamic, spatio-temporally regulated processes such as Golgi and nuclear envelope disassembly/reassembly, spindle apparatus formation, chromosome condensation and segregation, and cytoplasmic division. This chapter will describe practical methods for cell synchronization, selection of fluorescent markers for transfection, and setting up imaging conditions and microscope parameters for acquiring time-lapse images of the Golgi apparatus in mitotic cells. These are general methods that can be applied to the study of many different types of organelles and molecules in dividing cells.
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47
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Michaelson D, Abidi W, Guardavaccaro D, Zhou M, Ahearn I, Pagano M, Philips MR. Rac1 accumulates in the nucleus during the G2 phase of the cell cycle and promotes cell division. ACTA ACUST UNITED AC 2008; 181:485-96. [PMID: 18443222 PMCID: PMC2364699 DOI: 10.1083/jcb.200801047] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Rac1 regulates a wide variety of cellular processes. The polybasic region of the Rac1 C terminus functions both as a plasma membrane–targeting motif and a nuclear localization sequence (NLS). We show that a triproline N-terminal to the polybasic region contributes to the NLS, which is cryptic in the sense that it is strongly inhibited by geranylgeranylation of the adjacent cysteine. Subcellular fractionation demonstrated endogenous Rac1 in the nucleus and Triton X-114 partition revealed that this pool is prenylated. Cell cycle–blocking agents, synchronization of cells stably expressing low levels of GFP-Rac1, and time-lapse microscopy of asynchronous cells revealed Rac1 accumulation in the nucleus in late G2 and exclusion in early G1. Although constitutively active Rac1 restricted to the cytoplasm inhibited cell division, activated Rac1 expressed constitutively in the nucleus increased the mitotic rate. These results show that Rac1 cycles in and out of the nucleus during the cell cycle and thereby plays a role in promoting cell division.
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Affiliation(s)
- David Michaelson
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
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48
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Olenych SG, Claxton NS, Ottenberg GK, Davidson MW. The fluorescent protein color palette. ACTA ACUST UNITED AC 2008; Chapter 21:Unit 21.5. [PMID: 18228502 DOI: 10.1002/0471143030.cb2105s36] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Advances in fluorescent protein development over the past 10 years have led to fine-tuning of the Aequorea victoria jellyfish color palette in the emission color range from blue to yellow, while a significant amount of progress has been achieved with reef coral species in the generation of monomeric fluorescent proteins emitting in the orange to far-red spectral regions. It is not inconceivable that near-infrared fluorescent proteins loom on the horizon. Expansion of the fluorescent protein family to include optical highlighters and FRET biosensors further arms this ubiquitous class of fluorophores with biological probes capable of photoactivation, photoconversion, and detection of molecular interactions beyond the resolution limits of optical microscopy. The success of these endeavors certainly suggests that almost any biological parameter can be investigated using the appropriate fluorescent protein-based application.
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Ban KH, Torres JZ, Miller JJ, Mikhailov A, Nachury MV, Tung JJ, Rieder CL, Jackson PK. The END network couples spindle pole assembly to inhibition of the anaphase-promoting complex/cyclosome in early mitosis. Dev Cell 2007; 13:29-42. [PMID: 17609108 DOI: 10.1016/j.devcel.2007.04.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Revised: 02/09/2007] [Accepted: 04/23/2007] [Indexed: 10/23/2022]
Abstract
Cyclin-dependent kinase 1 (Cdk1) initiates mitosis and later activates the anaphase-promoting complex/cyclosome (APC/C) to destroy cyclins. Kinetochore-derived checkpoint signaling delays APC/C-dependent cyclin B destruction, and checkpoint-independent mechanisms cooperate to limit APC/C activity when kinetochores lack checkpoint components in early mitosis. The APC/C and cyclin B localize to the spindle and poles, but the significance and regulation of these populations remain unclear. Here we describe a critical spindle pole-associated mechanism, called the END (Emi1/NuMA/dynein-dynactin) network, that spatially restricts APC/C activity in early mitosis. The APC/C inhibitor Emi1 binds the spindle-organizing NuMA/dynein-dynactin complex to anchor and inhibit the APC/C at spindle poles, and thereby limits destruction of spindle-associated cyclin B. Cyclin B/Cdk1 activity recruits the END network and establishes a positive feedback loop to stabilize spindle-associated cyclin B critical for spindle assembly. The organization of the APC/C on the spindle also provides a framework for understanding microtubule-dependent organization of protein destruction.
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Affiliation(s)
- Kenneth H Ban
- Program in Cancer Biology, Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
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50
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Mora-Bermúdez F, Ellenberg J. Measuring structural dynamics of chromosomes in living cells by fluorescence microscopy. Methods 2007; 41:158-67. [PMID: 17189858 DOI: 10.1016/j.ymeth.2006.07.035] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Accepted: 07/11/2006] [Indexed: 10/23/2022] Open
Abstract
Mitotic and meiotic chromosomes are the compact packages that faithfully transport the genetic and epigenetic information to the following cell generations. How chromatin dynamically cycles between the decompacted interphase state that supports transcription and replication and the compacted state required for chromosome segregation is not understood. To address this long-standing problem, the structure of chromatin should ideally be studied in the physiological context of intact cells and organisms. We discuss here, the contributions that live-cell imaging can and has made to the study of mitotic chromosome compaction and highlight the power and limitations of this approach. We review methodologies used and suggest that combinatorial approaches and developing new imaging technologies will be key to shedding light on this long-standing question in cell biology.
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Affiliation(s)
- Felipe Mora-Bermúdez
- Gene Expression Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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