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Matejka N, Amarlou A, Neubauer J, Rudigkeit S, Reindl J. High-Resolution Microscopic Characterization of Tunneling Nanotubes in Living U87 MG and LN229 Glioblastoma Cells. Cells 2024; 13:464. [PMID: 38474428 DOI: 10.3390/cells13050464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024] Open
Abstract
Tunneling nanotubes (TNTs) are fine, nanometer-sized membrane connections between distant cells that provide an efficient communication tool for cellular organization. TNTs are thought to play a critical role in cellular behavior, particularly in cancer cells. The treatment of aggressive cancers such as glioblastoma remains challenging due to their high potential for developing therapy resistance, high infiltration rates, uncontrolled cell growth, and other aggressive features. A better understanding of the cellular organization via cellular communication through TNTs could help to find new therapeutic approaches. In this study, we investigate the properties of TNTs in two glioblastoma cell lines, U87 MG and LN229, including measurements of their diameter by high-resolution live-cell stimulated emission depletion (STED) microscopy and an analysis of their length, morphology, lifetime, and formation by live-cell confocal microscopy. In addition, we discuss how these fine compounds can ideally be studied microscopically. In particular, we show which membrane-labeling method is suitable for studying TNTs in glioblastoma cells and demonstrate that live-cell studies should be preferred to explore the role of TNTs in cellular behavior. Our observations on TNT formation in glioblastoma cells suggest that TNTs could be involved in cell migration and serve as guidance.
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Affiliation(s)
- Nicole Matejka
- Institute for Applied Physics and Measurement Technology, University of the Bundeswehr Munich, 85577 Neubiberg, Germany
| | - Asieh Amarlou
- Institute for Applied Physics and Measurement Technology, University of the Bundeswehr Munich, 85577 Neubiberg, Germany
| | - Jessica Neubauer
- Institute for Applied Physics and Measurement Technology, University of the Bundeswehr Munich, 85577 Neubiberg, Germany
| | - Sarah Rudigkeit
- Institute for Applied Physics and Measurement Technology, University of the Bundeswehr Munich, 85577 Neubiberg, Germany
| | - Judith Reindl
- Institute for Applied Physics and Measurement Technology, University of the Bundeswehr Munich, 85577 Neubiberg, Germany
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2
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Hansson A, Karlsen EA, Stensen W, Svendsen JSM, Berglin M, Lundgren A. Preventing E. coli Biofilm Formation with Antimicrobial Peptide-Functionalized Surface Coatings: Recognizing the Dependence on the Bacterial Binding Mode Using Live-Cell Microscopy. ACS Appl Mater Interfaces 2024; 16:6799-6812. [PMID: 38294883 PMCID: PMC10875647 DOI: 10.1021/acsami.3c16004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Antimicrobial peptides (AMPs) can kill bacteria by destabilizing their membranes, yet translating these molecules' properties into a covalently attached antibacterial coating is challenging. Rational design efforts are obstructed by the fact that standard microbiology methods are ill-designed for the evaluation of coatings, disclosing few details about why grafted AMPs function or do not function. It is particularly difficult to distinguish the influence of the AMP's molecular structure from other factors controlling the total exposure, including which type of bonds are formed between bacteria and the coating and how persistent these contacts are. Here, we combine label-free live-cell microscopy, microfluidics, and automated image analysis to study the response of surface-bound Escherichia coli challenged by the same small AMP either in solution or grafted to the surface through click chemistry. Initially after binding, the grafted AMPs inhibited bacterial growth more efficiently than did AMPs in solution. Yet, after 1 h, E. coli on the coated surfaces increased their expression of type-1 fimbriae, leading to a change in their binding mode, which diminished the coating's impact. The wealth of information obtained from continuously monitoring the growth, shape, and movements of single bacterial cells allowed us to elucidate and quantify the different factors determining the antibacterial efficacy of the grafted AMPs. We expect this approach to aid the design of elaborate antibacterial material coatings working by specific and selective actions, not limited to contact-killing. This technology is needed to support health care and food production in the postantibiotic era.
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Affiliation(s)
- Adam Hansson
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Department
of Chemistry and Materials, RISE Research
Institutes of Sweden, Borås 50115, Sweden
| | - Eskil André Karlsen
- Amicoat
A/S, Sykehusvegen 23, Tromsø 9019, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Wenche Stensen
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - John S. M. Svendsen
- Amicoat
A/S, Sykehusvegen 23, Tromsø 9019, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Mattias Berglin
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Department
of Chemistry and Materials, RISE Research
Institutes of Sweden, Borås 50115, Sweden
| | - Anders Lundgren
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Centre
for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg 41346, Sweden
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3
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Grosse-Holz S. The searchable chromosome. Trends Genet 2023; 39:895-896. [PMID: 37690888 DOI: 10.1016/j.tig.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]
Abstract
To date, genome structure and dynamics have been studied mostly independently; their interplay is a notable blind spot of the field. Brückner, Chen, et al. recently demonstrated an integrated experimental approach sensitive to both, uncovering a striking robustness of enhancer-promoter search times (dynamics) to changes in genomic separation (structure).
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Affiliation(s)
- Simon Grosse-Holz
- Center for Systems Biology Dresden, Pfotenhauerstraße 108, 01307 Dresden, Germany; Max-Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany.
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4
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Constantinou I, Bastounis EE. Cell-stretching devices: advances and challenges in biomedical research and live-cell imaging. Trends Biotechnol 2023; 41:939-950. [PMID: 36604290 DOI: 10.1016/j.tibtech.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/29/2022] [Accepted: 12/09/2022] [Indexed: 01/04/2023]
Abstract
Basic human functions such as breathing and digestion require mechanical stretching of cells and tissues. However, when it comes to laboratory experiments, the mechanical stretching that cells experience in the body is not often replicated, limiting the biomimetic nature of the studies and the relevance of results. Herein, we establish the importance of mechanical stretching during in vitro investigations by reviewing seminal works performed using cell-stretching platforms, highlighting important outcomes of these works as well as the engineering characteristics of the platforms used. Emphasis is placed on the compatibility of cell-stretching devices (CSDs) with live-cell imaging as well as their limitations and on the research advancements that could arise from live-cell imaging performed during cell stretching.
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Affiliation(s)
- Iordania Constantinou
- Institute of Microtechnology (IMT), Technische Universität Braunschweig, Alte Salzdahlumer Str. 203, 38124 Braunschweig, Germany; Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
| | - Effie E Bastounis
- Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections" EXC 2124, Eberhard Karls University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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5
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Attram HD, Korkor CM, Taylor D, Njoroge M, Chibale K. Antimalarial Imidazopyridines Incorporating an Intramolecular Hydrogen Bonding Motif: Medicinal Chemistry and Mechanistic Studies. ACS Infect Dis 2023; 9:928-942. [PMID: 36946433 PMCID: PMC10111423 DOI: 10.1021/acsinfecdis.2c00584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
We previously identified a novel class of antimalarial benzimidazoles incorporating an intramolecular hydrogen bonding motif. The frontrunner of the series, analogue A, showed nanomolar activity against the chloroquine-sensitive NF54 and multi-drug-resistant K1 strains of Plasmodium falciparum (PfNF54 IC50 = 0.079 μM; PfK1 IC50 = 0.335 μM). Here, we describe a cell-based medicinal chemistry structure-activity relationship study using compound A as a basis. This effort led to the identification of novel antimalarial imidazopyridines with activities of <1 μM, favorable cytotoxicity profiles, and good physicochemical properties. Analogue 14 ( PfNF54 IC50 = 0.08 μM; PfK1 IC50 = 0.10 μM) was identified as the frontrunner of the series. Preliminary mode of action studies employing molecular docking, live-cell confocal microscopy, and a cellular heme fractionation assay revealed that 14 does not directly inhibit the conversion of heme to hemozoin, although it could be involved in other processes in the parasite's digestive vacuole.
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Affiliation(s)
- Henrietta D Attram
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Constance M Korkor
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Dale Taylor
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Mathew Njoroge
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
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6
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Abstract
Biological discovery has been driven by advances in throughput and resolution of analysis technologies. They have also created an indelible bias for snapshot-based knowledge. Even though recent methods such as multi-omics single-cell assays have empowered immunological investigations, they still provide snapshots of cellular behaviors and thus, have inherent limitations in reconstructing unsynchronized dynamic events across individual cells. Here, we present a rationale for how NF-κB may convey specificity of contextual information through subtle quantitative features of its signaling dynamics. The next frontier of predictive understanding should involve functional characterization of NF-κB signaling dynamics and their immunological implications. This may help solve the apparent paradox that a ubiquitously activated transcription factor can shape accurate responses to different immune challenges.
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Affiliation(s)
- Mohammad Aqdas
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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7
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Goldberger O, Szoke T, Nussbaum-Shochat A, Amster-Choder O. Heterotypic phase separation of Hfq is linked to its roles as an RNA chaperone. Cell Rep 2022; 41:111881. [PMID: 36577380 DOI: 10.1016/j.celrep.2022.111881] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 11/25/2022] [Accepted: 12/03/2022] [Indexed: 12/29/2022] Open
Abstract
Hfq, an Sm-like protein and the major RNA chaperone in E. coli, has been shown to distribute non-uniformly along a helical path under normal growth conditions and to relocate to the cell poles under certain stress conditions. We have previously shown that Hfq relocation to the poles is accompanied by polar accumulation of most small RNAs (sRNAs). Here, we show that Hfq undergoes RNA-dependent phase separation to form cytoplasmic or polar condensates of different density under normal and stress conditions, respectively. Purified Hfq forms droplets in the presence of crowding agents or RNA, indicating that its condensation is via heterotypic interactions. Stress-induced relocation of Hfq condensates and sRNAs to the poles depends on the pole-localizer TmaR. Phase separation of Hfq correlates with its ability to perform its posttranscriptional roles as sRNA-stabilizer and sRNA-mRNA matchmaker. Our study offers a spatiotemporal mechanism for sRNA-mediated regulation in response to environmental changes.
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Affiliation(s)
- Omer Goldberger
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel
| | - Tamar Szoke
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel
| | - Anat Nussbaum-Shochat
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel.
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8
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Robitaille MC, Christodoulides JA, Calhoun PJ, Byers JM, Raphael MP. Interfacing Live Cells with Surfaces: A Concurrent Control Technique for Quantifying Surface Ligand Activity. ACS Appl Bio Mater 2021; 4:7856-7864. [PMID: 35006767 DOI: 10.1021/acsabm.1c00797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surface ligand activity is a key design parameter for successfully interfacing surfaces with cells─whether in the context of in vitro investigations for understanding cellular signaling pathways or more applied applications in drug delivery and medical implants. Unlike other crucial surface parameters, such as stiffness and roughness, surface ligand activity is typically based on a set of assumptions rather than directly measured, giving rise to interpretations of cell adhesion that can vary with the assumptions made. To fill this void, we have developed a concurrent control technique for directly characterizing in vitro ligand surface activity. Pairs of gold-coated glass chips were biofunctionalized with RGD ligand in a parallel workflow: one chip for in vitro applications and the other for surface plasmon resonance (SPR)-based RGD activity characterization. Recombinant αVβ3 integrins were injected over the SPR chip surface as mimics of the cellular-membrane-bound receptors and the resulting binding kinetics parameterized to quantify surface ligand activity. These activity measurements were correlated with cell morphological features, measured by interfacing MDA-MB-231 cells with the in vitro chip surfaces on the live cell microscope. We demonstrate how the interpretation of a cell phenotype based on direct activity measurements can vary markedly from interpretations based on assumed activity. The SPR concurrent control approach has multiple advantages due to the fact that SPR is a standardized technique and has the sensitivity to measure ligand activity across the most relevant range of extracellular surface densities, while the in vitro chip design can be used with all commonly used light microscopy modalities (e.g., phase contrast, DIC, and fluorescence) so that a wide range of phenotypic and molecular markers can be correlated to the ligand surface activity.
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Affiliation(s)
- Michael C Robitaille
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375-5320, United States
| | | | | | - Jeff M Byers
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375-5320, United States
| | - Marc P Raphael
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375-5320, United States
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9
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Pessoa J. Live-cell visualization of cytochrome c: a tool to explore apoptosis. Biochem Soc Trans 2021:BST20211028. [PMID: 34747968 DOI: 10.1042/BST20211028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023]
Abstract
Apoptosis dysfunction is associated with several malignancies, including cancer and autoimmune diseases. Apoptosis restoration could be an attractive therapeutic approach to those diseases. Mitochondrial outer membrane permeabilization is regarded as the point of no return in the 'classical' apoptosis triggering pathway. Cytoplasmic release of cytochrome c (cyt c), a mitochondrial electron transporter, is a prominent indicator of such critical step. Therefore, visualizing cyt c efflux in living cells is a convenient approach to address apoptosis triggering and monitor performance of apoptosis restoration strategies. Recent years have been prolific in the development of biosensors to visualize cyt c mitochondrial efflux in living cells, by fluorescence microscopy. These biosensors specifically detect endogenous, untagged cyt c, while showing efficient cellular uptake and reduced cell toxicity. A common aspect is their fluorescence quenching in the absence or presence of bound cyt c, resulting in two main biosensor types: 'turn ON' and 'turn OFF'. In some of these systems, fluorescence intensity of fluorophore-bound aptamers is enhanced upon cyt c binding. In others, cyt c binding to quantum dots quenches their fluorescence. In the present minireview, I describe these biosensors and briefly introduce some hypotheses that could be addressed using these novel tools.
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10
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Colin A, Micali G, Faure L, Cosentino Lagomarsino M, van Teeffelen S. Two different cell-cycle processes determine the timing of cell division in Escherichia coli. eLife 2021; 10:67495. [PMID: 34612203 PMCID: PMC8555983 DOI: 10.7554/elife.67495] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Cells must control the cell cycle to ensure that key processes are brought to completion. In Escherichia coli, it is controversial whether cell division is tied to chromosome replication or to a replication-independent inter-division process. A recent model suggests instead that both processes may limit cell division with comparable odds in single cells. Here, we tested this possibility experimentally by monitoring single-cell division and replication over multiple generations at slow growth. We then perturbed cell width, causing an increase of the time between replication termination and division. As a consequence, replication became decreasingly limiting for cell division, while correlations between birth and division and between subsequent replication-initiation events were maintained. Our experiments support the hypothesis that both chromosome replication and a replication-independent inter-division process can limit cell division: the two processes have balanced contributions in non-perturbed cells, while our width perturbations increase the odds of the replication-independent process being limiting.
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Affiliation(s)
- Alexandra Colin
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France
| | - Gabriele Micali
- Department of Environmental Microbiology, Dübendorf, Switzerland.,Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Louis Faure
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France
| | - Marco Cosentino Lagomarsino
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy.,Physics Department, University of Milan, and INFN, Milan, Italy
| | - Sven van Teeffelen
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Canada
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11
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Touizer E, Sieben C, Henriques R, Marsh M, Laine RF. Application of Super-Resolution and Advanced Quantitative Microscopy to the Spatio-Temporal Analysis of Influenza Virus Replication. Viruses 2021; 13:233. [PMID: 33540739 PMCID: PMC7912985 DOI: 10.3390/v13020233] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023] Open
Abstract
With an estimated three to five million human cases annually and the potential to infect domestic and wild animal populations, influenza viruses are one of the greatest health and economic burdens to our society, and pose an ongoing threat of large-scale pandemics. Despite our knowledge of many important aspects of influenza virus biology, there is still much to learn about how influenza viruses replicate in infected cells, for instance, how they use entry receptors or exploit host cell trafficking pathways. These gaps in our knowledge are due, in part, to the difficulty of directly observing viruses in living cells. In recent years, advances in light microscopy, including super-resolution microscopy and single-molecule imaging, have enabled many viral replication steps to be visualised dynamically in living cells. In particular, the ability to track single virions and their components, in real time, now allows specific pathways to be interrogated, providing new insights to various aspects of the virus-host cell interaction. In this review, we discuss how state-of-the-art imaging technologies, notably quantitative live-cell and super-resolution microscopy, are providing new nanoscale and molecular insights into influenza virus replication and revealing new opportunities for developing antiviral strategies.
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Affiliation(s)
- Emma Touizer
- Division of Infection and Immunity, University College London, London WC1E 6AE, UK;
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Christian Sieben
- Department of Cell Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Romain F. Laine
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
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12
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Meyer M, Paquet A, Arguel MJ, Peyre L, Gomes-Pereira LC, Lebrigand K, Mograbi B, Brest P, Waldmann R, Barbry P, Hofman P, Roux J. Profiling the Non-genetic Origins of Cancer Drug Resistance with a Single-Cell Functional Genomics Approach Using Predictive Cell Dynamics. Cell Syst 2020; 11:367-374.e5. [PMID: 33099406 DOI: 10.1016/j.cels.2020.08.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/12/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
Non-genetic heterogeneity observed in clonal cell populations is an immediate cause of drug resistance that remains challenging to profile because of its transient nature. Here, we coupled three single-cell technologies to link the predicted drug response of a cell to its own genome-wide transcriptomic profile. As a proof of principle, we analyzed the response to tumor-necrosis-factor-related apoptosis-inducing ligand (TRAIL) in HeLa cells to demonstrate that cell dynamics can discriminate the transient transcriptional states at the origin of cell decisions such as sensitivity and resistance. Our same-cell approach, named fate-seq, can reveal the molecular factors regulating the efficacy of a drug in clonal cells, providing therapeutic targets of non-genetic drug resistance otherwise confounded in gene expression noise. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Mickael Meyer
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France
| | - Agnès Paquet
- Université Côte d'Azur, CNRS UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, 06560 Nice, France
| | - Marie-Jeanne Arguel
- Université Côte d'Azur, CNRS UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, 06560 Nice, France
| | - Ludovic Peyre
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France
| | - Luis C Gomes-Pereira
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, 06560 Nice, France
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, 06560 Nice, France
| | - Baharia Mograbi
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France
| | - Patrick Brest
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France
| | - Rainer Waldmann
- Université Côte d'Azur, CNRS UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, 06560 Nice, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, 06560 Nice, France
| | - Paul Hofman
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France
| | - Jérémie Roux
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France.
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13
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Muhtadi R, Lorenz A, Mpaulo SJ, Siebenwirth C, Scherthan H. Catalase T-Deficient Fission Yeast Meiocytes Show Resistance to Ionizing Radiation. Antioxidants (Basel) 2020; 9:antiox9090881. [PMID: 32957622 PMCID: PMC7555645 DOI: 10.3390/antiox9090881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/20/2022] Open
Abstract
Environmental stress, reactive oxygen species (ROS), or ionizing radiation (IR) can induce adverse effects in organisms and their cells, including mutations and premature aging. DNA damage and its faulty repair can lead to cell death or promote cancer through the accumulation of mutations. Misrepair in germ cells is particularly dangerous as it may lead to alterations in developmental programs and genetic disease in the offspring. DNA damage pathways and radical defense mechanisms mediate resistance to genotoxic stresses. Here, we investigated, in the fission yeast Schizosaccharomyces pombe, the role of the H2O2-detoxifying enzyme cytosolic catalase T (Ctt1) and the Fe2+/Mn2+ symporter Pcl1 in protecting meiotic chromosome dynamics and gamete formation from radicals generated by ROS and IR. We found that wild-type and pcl1-deficient cells respond similarly to X ray doses of up to 300 Gy, while ctt1∆ meiocytes showed a moderate sensitivity to IR but a hypersensitivity to hydrogen peroxide with cells dying at >0.4 mM H2O2. Meiocytes deficient for pcl1, on the other hand, showed a resistance to hydrogen peroxide similar to that of the wild type, surviving doses >40 mM. In all, it appears that in the absence of the main H2O2-detoxifying pathway S. pombe meiocytes are able to survive significant doses of IR-induced radicals.
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Affiliation(s)
- Razan Muhtadi
- Institut für Radiobiologie der Bundeswehr in Verb. mit der Universität Ulm, Neuherbergstr. 11, D-80937 Munich, Germany; (R.M.); (C.S.)
| | - Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (A.L.); (S.J.M.)
| | - Samantha J. Mpaulo
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (A.L.); (S.J.M.)
| | - Christian Siebenwirth
- Institut für Radiobiologie der Bundeswehr in Verb. mit der Universität Ulm, Neuherbergstr. 11, D-80937 Munich, Germany; (R.M.); (C.S.)
| | - Harry Scherthan
- Institut für Radiobiologie der Bundeswehr in Verb. mit der Universität Ulm, Neuherbergstr. 11, D-80937 Munich, Germany; (R.M.); (C.S.)
- Correspondence: ; Tel.: +49-89-992692-2272
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14
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Roobol SJ, van den Bent I, van Cappellen WA, Abraham TE, Paul MW, Kanaar R, Houtsmuller AB, van Gent DC, Essers J. Comparison of High- and Low-LET Radiation-Induced DNA Double-Strand Break Processing in Living Cells. Int J Mol Sci 2020; 21:E6602. [PMID: 32917044 DOI: 10.3390/ijms21186602] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/26/2020] [Accepted: 09/06/2020] [Indexed: 12/11/2022] Open
Abstract
High-linear-energy-transfer (LET) radiation is more lethal than similar doses of low-LET radiation types, probably a result of the condensed energy deposition pattern of high-LET radiation. Here, we compare high-LET α-particle to low-LET X-ray irradiation and monitor double-strand break (DSB) processing. Live-cell microscopy was used to monitor DNA double-strand breaks (DSBs), marked by p53-binding protein 1 (53BP1). In addition, the accumulation of the endogenous 53BP1 and replication protein A (RPA) DSB processing proteins was analyzed by immunofluorescence. In contrast to α-particle-induced 53BP1 foci, X-ray-induced foci were resolved quickly and more dynamically as they showed an increase in 53BP1 protein accumulation and size. In addition, the number of individual 53BP1 and RPA foci was higher after X-ray irradiation, while focus intensity was higher after α-particle irradiation. Interestingly, 53BP1 foci induced by α-particles contained multiple RPA foci, suggesting multiple individual resection events, which was not observed after X-ray irradiation. We conclude that high-LET α-particles cause closely interspaced DSBs leading to high local concentrations of repair proteins. Our results point toward a change in DNA damage processing toward DNA end-resection and homologous recombination, possibly due to the depletion of soluble protein in the nucleoplasm. The combination of closely interspaced DSBs and perturbed DNA damage processing could be an explanation for the increased relative biological effectiveness (RBE) of high-LET α-particles compared to X-ray irradiation.
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15
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Abstract
Mitochondria are essential for eukaryotic life. These double-membrane organelles often form highly dynamic tubular networks interacting with many cellular structures. Their highly convoluted contiguous inner membrane compartmentalizes the organelle, which is crucial for mitochondrial function. Since the diameter of the mitochondrial tubules is generally close to the diffraction limit of light microscopy, it is often challenging, if not impossible, to visualize submitochondrial structures or protein distributions using conventional light microscopy. This renders super-resolution microscopy particularly valuable, and attractive, for studying mitochondria. Super-resolution microscopy encompasses a diverse set of approaches that extend resolution, as well as nanoscopy techniques that can even overcome the diffraction limit. In this review, we provide an overview of recent studies using super-resolution microscopy to investigate mitochondria, discuss the strengths and opportunities of the various methods in addressing specific questions in mitochondrial biology, and highlight potential future developments.
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Affiliation(s)
- Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
- Clinic of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Till Stephan
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
- Clinic of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Peter Ilgen
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
- Clinic of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Christian Brüser
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
- Clinic of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
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16
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Kannaiah S, Livny J, Amster-Choder O. Spatiotemporal Organization of the E. coli Transcriptome: Translation Independence and Engagement in Regulation. Mol Cell 2019; 76:574-589.e7. [PMID: 31540875 DOI: 10.1016/j.molcel.2019.08.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 06/28/2019] [Accepted: 08/13/2019] [Indexed: 12/22/2022]
Abstract
RNA localization in eukaryotes is a mechanism to regulate transcripts fate. Conversely, bacterial transcripts were not assumed to be specifically localized. We previously demonstrated that E. coli mRNAs may localize to where their products localize in a translation-independent manner, thus challenging the transcription-translation coupling extent. However, the scope of RNA localization in bacteria remained unknown. Here, we report the distribution of the E. coli transcriptome between the membrane, cytoplasm, and poles by combining cell fractionation with deep-sequencing (Rloc-seq). Our results reveal asymmetric RNA distribution on a transcriptome-wide scale, significantly correlating with proteome localization and prevalence of translation-independent RNA localization. The poles are enriched with stress-related mRNAs and small RNAs, the latter becoming further enriched upon stress in an Hfq-dependent manner. Genome organization may play a role in localizing membrane protein-encoding transcripts. Our results show an unexpected level of intricacy in bacterial transcriptome organization and highlight the poles as hubs for regulation.
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Affiliation(s)
- Shanmugapriya Kannaiah
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02140, USA
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel.
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17
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Escorcia W, Shen KF, Yuan JP, Forsburg SL. Examination of Mitotic and Meiotic Fission Yeast Nuclear Dynamics by Fluorescence Live-cell Microscopy. J Vis Exp 2019:10.3791/59822. [PMID: 31282894 PMCID: PMC6701690 DOI: 10.3791/59822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Live-cell imaging is a microscopy technique used to examine cell and protein dynamics in living cells. This imaging method is not toxic, generally does not interfere with cell physiology, and requires minimal experimental handling. The low levels of technical interference enable researchers to study cells across multiple cycles of mitosis and to observe meiosis from beginning to end. Using fluorescent tags such as Green Fluorescent Protein (GFP) and Red Fluorescent Protein (RFP), researchers can analyze different factors whose functions are important for processes like transcription, DNA replication, cohesion, and segregation. Coupled with data analysis using Fiji (a free, optimized ImageJ version), live-cell imaging offers various ways of assessing protein movement, localization, stability, and timing, as well as nuclear dynamics and chromosome segregation. However, as is the case with other microscopy methods, live-cell imaging is limited by the intrinsic properties of light, which put a limit to the resolution power at high magnifications, and is also sensitive to photobleaching or phototoxicity at high wavelength frequencies. However, with some care, investigators can bypass these physical limitations by carefully choosing the right conditions, strains, and fluorescent markers to allow for the appropriate visualization of mitotic and meiotic events.
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Affiliation(s)
- Wilber Escorcia
- Program in Molecular and Computational Biology, University of Southern California; Leonard Davis School of Gerontology, University of Southern California
| | - Kuo-Fang Shen
- Program in Molecular and Computational Biology, University of Southern California
| | - Ji-Ping Yuan
- Program in Molecular and Computational Biology, University of Southern California
| | - Susan L Forsburg
- Program in Molecular and Computational Biology, University of Southern California;
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18
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Alanine DGW, Quinkert D, Kumarasingha R, Mehmood S, Donnellan FR, Minkah NK, Dadonaite B, Diouf A, Galaway F, Silk SE, Jamwal A, Marshall JM, Miura K, Foquet L, Elias SC, Labbé GM, Douglas AD, Jin J, Payne RO, Illingworth JJ, Pattinson DJ, Pulido D, Williams BG, de Jongh WA, Wright GJ, Kappe SHI, Robinson CV, Long CA, Crabb BS, Gilson PR, Higgins MK, Draper SJ. Human Antibodies that Slow Erythrocyte Invasion Potentiate Malaria-Neutralizing Antibodies. Cell 2019; 178:216-228.e21. [PMID: 31204103 PMCID: PMC6602525 DOI: 10.1016/j.cell.2019.05.025] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 03/05/2019] [Accepted: 05/13/2019] [Indexed: 12/30/2022]
Abstract
The Plasmodium falciparum reticulocyte-binding protein homolog 5 (PfRH5) is the leading target for next-generation vaccines against the disease-causing blood-stage of malaria. However, little is known about how human antibodies confer functional immunity against this antigen. We isolated a panel of human monoclonal antibodies (mAbs) against PfRH5 from peripheral blood B cells from vaccinees in the first clinical trial of a PfRH5-based vaccine. We identified a subset of mAbs with neutralizing activity that bind to three distinct sites and another subset of mAbs that are non-functional, or even antagonistic to neutralizing antibodies. We also identify the epitope of a novel group of non-neutralizing antibodies that significantly reduce the speed of red blood cell invasion by the merozoite, thereby potentiating the effect of all neutralizing PfRH5 antibodies as well as synergizing with antibodies targeting other malaria invasion proteins. Our results provide a roadmap for structure-guided vaccine development to maximize antibody efficacy against blood-stage malaria.
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Affiliation(s)
- Daniel G W Alanine
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Doris Quinkert
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | | | - Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Francesca R Donnellan
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Nana K Minkah
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Ave. N., #500, Seattle, WA 98109, USA
| | - Bernadeta Dadonaite
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Ababacar Diouf
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Francis Galaway
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Sarah E Silk
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Abhishek Jamwal
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jennifer M Marshall
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Lander Foquet
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Ave. N., #500, Seattle, WA 98109, USA
| | - Sean C Elias
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Geneviève M Labbé
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Alexander D Douglas
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Jing Jin
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Ruth O Payne
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Joseph J Illingworth
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - David J Pattinson
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - David Pulido
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Barnabas G Williams
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Willem A de Jongh
- ExpreS(2)ion Biotechnologies, SCION-DTU Science Park, Agern Allé 1, Hørsholm 2970, Denmark
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Stefan H I Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Ave. N., #500, Seattle, WA 98109, USA
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Carole A Long
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Brendan S Crabb
- Burnet Institute, 85 Commercial Road, Melbourne, VIC 3004, Australia
| | - Paul R Gilson
- Burnet Institute, 85 Commercial Road, Melbourne, VIC 3004, Australia
| | - Matthew K Higgins
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Simon J Draper
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK.
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19
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Abstract
Genetically encoded live-cell reporters measure signaling pathway activity at the cellular level with high temporal resolution, often revealing a high degree of cell-to-cell heterogeneity. By using multiple spectrally distinct reporters within the same cell, signal transmission from one node to another within a signaling pathway can be analyzed to quantify factors such as signaling efficiency and delay. With other reporter configurations, correlation between different signaling pathways can be quantified. Such analyses can be used to establish the mechanisms and consequences of cell-to-cell heterogeneity and can inform new models of the functional properties of signaling pathways. In this unit, we describe an approach for designing and executing live-cell multiplexed reporter experiments. We also describe approaches for analyzing the resulting time-course data to quantify correlations and trends between the measured parameters at the single-cell level. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California
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20
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Liao Y, Rust MJ. The Min Oscillator Defines Sites of Asymmetric Cell Division in Cyanobacteria during Stress Recovery. Cell Syst 2018; 7:471-481.e6. [PMID: 30414921 DOI: 10.1016/j.cels.2018.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/04/2018] [Accepted: 10/15/2018] [Indexed: 11/20/2022]
Abstract
When resources are abundant, many rod-shaped bacteria reproduce through precise, symmetric divisions. However, realistic environments entail fluctuations between restrictive and permissive growth conditions. Here, we use time-lapse microscopy to study the division of the cyanobacterium Synechococcus elongatus as illumination intensity varies. We find that dim conditions produce elongated cells whose divisions follow a simple rule: cells shorter than ∼8 μm divide symmetrically, but above this length divisions become asymmetric, typically producing a short ∼3-μm daughter. We show that this division strategy is implemented by the Min system, which generates multi-node patterns and traveling waves in longer cells that favor the production of a short daughter. Mathematical modeling reveals that the feedback loops that create oscillatory Min patterns are needed to implement these generalized cell division rules. Thus, the Min system, which enforces symmetric divisions in short cells, acts to strongly suppress mid-cell divisions when S. elongatus cells are long.
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21
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Yakimovich A, Witte R, Andriasyan V, Georgi F, Greber UF. Label-Free Digital Holo-tomographic Microscopy Reveals Virus-Induced Cytopathic Effects in Live Cells. mSphere 2018; 3:e00599-18. [PMID: 30463927 DOI: 10.1128/mSphereDirect.00599-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
This study introduces label-free digital holo-tomographic microscopy (DHTM) and refractive index gradient (RIG) measurements of live, virus-infected cells. We use DHTM to describe virus type-specific cytopathic effects, including cyclic volume changes of vaccinia virus infections, and cytoplasmic condensations in herpesvirus and rhinovirus infections, distinct from apoptotic cells. This work shows for the first time that DHTM is suitable to observe virus-infected cells and distinguishes virus type-specific signatures under noninvasive conditions. It provides a basis for future studies, where correlative fluorescence microscopy of cell and virus structures annotate distinct RIG values derived from DHTM. Cytopathic effects (CPEs) are a hallmark of infections. CPEs are difficult to observe due to phototoxicity from classical light microscopy. We report distinct patterns of virus infections in live cells using digital holo-tomographic microscopy (DHTM). DHTM is label-free and records the phase shift of low-energy light passing through the specimen on a transparent surface with minimal perturbation. DHTM measures the refractive index (RI) and computes the refractive index gradient (RIG), unveiling optical heterogeneity in cells. We find that vaccinia virus (VACV), herpes simplex virus (HSV), and rhinovirus (RV) infections progressively and distinctly increased RIG. VACV infection, but not HSV and RV infections, induced oscillations of cell volume, while all three viruses altered cytoplasmic membrane dynamics and induced apoptotic features akin to those caused by the chemical compound staurosporine. In sum, we introduce DHTM for quantitative label-free microscopy in infection research and uncover virus type-specific changes and CPE in living cells with minimal interference. IMPORTANCE This study introduces label-free digital holo-tomographic microscopy (DHTM) and refractive index gradient (RIG) measurements of live, virus-infected cells. We use DHTM to describe virus type-specific cytopathic effects, including cyclic volume changes of vaccinia virus infections, and cytoplasmic condensations in herpesvirus and rhinovirus infections, distinct from apoptotic cells. This work shows for the first time that DHTM is suitable to observe virus-infected cells and distinguishes virus type-specific signatures under noninvasive conditions. It provides a basis for future studies, where correlative fluorescence microscopy of cell and virus structures annotate distinct RIG values derived from DHTM.
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22
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Turkowyd B, Balinovic A, Virant D, Carnero HGG, Caldana F, Endesfelder M, Bourgeois D, Endesfelder U. A General Mechanism of Photoconversion of Green-to-Red Fluorescent Proteins Based on Blue and Infrared Light Reduces Phototoxicity in Live-Cell Single-Molecule Imaging. Angew Chem Int Ed Engl 2017; 56:11634-11639. [PMID: 28574633 DOI: 10.1002/anie.201702870] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/27/2017] [Indexed: 11/09/2022]
Abstract
Photoconversion of fluorescent proteins by blue and complementary near-infrared light, termed primed conversion (PC), is a mechanism recently discovered for Dendra2. We demonstrate that controlling the conformation of arginine at residue 66 by threonine at residue 69 of fluorescent proteins from Anthozoan families (Dendra2, mMaple, Eos, mKikGR, pcDronpa protein families) represents a general route to facilitate PC. Mutations of alanine 159 or serine 173, which are known to influence chromophore flexibility and allow for reversible photoswitching, prevent PC. In addition, we report enhanced photoconversion for pcDronpa variants with asparagine 116. We demonstrate live-cell single-molecule imaging with reduced phototoxicity using PC and record trajectories of RNA polymerase in Escherichia coli cells.
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Affiliation(s)
- Bartosz Turkowyd
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Alexander Balinovic
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - David Virant
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Haruko G Gölz Carnero
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Fabienne Caldana
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Marc Endesfelder
- Institut für Assyriologie, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539, München, Germany
| | - Dominique Bourgeois
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044, Grenoble, France
| | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
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23
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Sukenik S, Ren P, Gruebele M. Weak protein-protein interactions in live cells are quantified by cell-volume modulation. Proc Natl Acad Sci U S A 2017; 114:6776-81. [PMID: 28607089 DOI: 10.1073/pnas.1700818114] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Weakly bound protein complexes play a crucial role in metabolic, regulatory, and signaling pathways, due in part to the high tunability of their bound and unbound populations. This tunability makes weak binding (micromolar to millimolar dissociation constants) difficult to quantify under biologically relevant conditions. Here, we use rapid perturbation of cell volume to modulate the concentration of weakly bound protein complexes, allowing us to detect their dissociation constant and stoichiometry directly inside the cell. We control cell volume by modulating media osmotic pressure and observe the resulting complex association and dissociation by FRET microscopy. We quantitatively examine the interaction between GAPDH and PGK, two sequential enzymes in the glycolysis catalytic cycle. GAPDH and PGK have been shown to interact weakly, but the interaction has not been quantified in vivo. A quantitative model fits our experimental results with log Kd = -9.7 ± 0.3 and a 2:1 prevalent stoichiometry of the GAPDH:PGK complex. Cellular volume perturbation is a widely applicable tool to detect transient protein interactions and other biomolecular interactions in situ. Our results also suggest that cells could use volume change (e.g., as occurs upon entry to mitosis) to regulate function by altering biomolecular complex concentrations.
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24
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Muster B, Rapp A, Cardoso MC. Systematic analysis of DNA damage induction and DNA repair pathway activation by continuous wave visible light laser micro-irradiation. AIMS Genet 2017; 4:47-68. [PMID: 31435503 PMCID: PMC6690239 DOI: 10.3934/genet.2017.1.47] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/16/2017] [Indexed: 01/19/2023]
Abstract
Laser micro-irradiation can be used to induce DNA damage with high spatial and temporal resolution, representing a powerful tool to analyze DNA repair in vivo in the context of chromatin. However, most lasers induce a mixture of DNA damage leading to the activation of multiple DNA repair pathways and making it impossible to study individual repair processes. Hence, we aimed to establish and validate micro-irradiation conditions together with inhibition of several key proteins to discriminate different types of DNA damage and repair pathways using lasers commonly available in confocal microscopes. Using time-lapse analysis of cells expressing fluorescently tagged repair proteins and also validation of the DNA damage generated by micro-irradiation using several key damage markers, we show that irradiation with a 405 nm continuous wave laser lead to the activation of all repair pathways even in the absence of exogenous sensitization. In contrast, we found that irradiation with 488 nm laser lead to the selective activation of non-processive short-patch base excision and single strand break repair, which were further validated by PARP inhibition and metoxyamine treatment. We conclude that these low energy conditions discriminated against processive long-patch base excision repair, nucleotide excision repair as well as double strand break repair pathways.
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Affiliation(s)
- Britta Muster
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Alexander Rapp
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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25
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Medina SH, Miller SE, Keim AI, Gorka AP, Schnermann MJ, Schneider JP. An Intrinsically Disordered Peptide Facilitates Non-Endosomal Cell Entry. Angew Chem Int Ed Engl 2016; 55:3369-72. [PMID: 26835878 DOI: 10.1002/anie.201510518] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/14/2015] [Indexed: 01/03/2023]
Abstract
Many cell-penetrating peptides (CPPs) fold at cell surfaces, adopting α- or β-structure that enable their intracellular transport. However, the same structural folds that facilitate cellular entry can also elicit potent membrane-lytic activity, limiting their use in delivery applications. Further, a distinct CPP can enter cells through many mechanisms, often leading to endosomal entrapment. Herein, we describe an intrinsically disordered peptide (CLIP6) that exclusively employs non-endosomal mechanisms to cross cellular membranes, while being remarkably biocompatible and serum-stable. We show that a single anionic glutamate residue is responsible for maintaining the disordered bioactive state of the peptide, defines its mechanism of cellular entry, and is central to its biocompatibility. CLIP6 can deliver membrane-impermeable cargo directly to the cytoplasm of cells, suggesting its broad utility for delivery of drug candidates limited by poor cell permeability and endosomal degradation.
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Affiliation(s)
- Scott H Medina
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Stephen E Miller
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Allison I Keim
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Alexander P Gorka
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Martin J Schnermann
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Joel P Schneider
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA.
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Nischan N, Herce HD, Natale F, Bohlke N, Budisa N, Cardoso MC, Hackenberger CPR. Covalent attachment of cyclic TAT peptides to GFP results in protein delivery into live cells with immediate bioavailability. Angew Chem Int Ed Engl 2014; 54:1950-3. [PMID: 25521313 DOI: 10.1002/anie.201410006] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Indexed: 11/08/2022]
Abstract
The delivery of free molecules into the cytoplasm and nucleus by using arginine-rich cell-penetrating peptides (CPPs) has been limited to small cargoes, while large cargoes such as proteins are taken up and trapped in endocytic vesicles. Based on recent work, in which we showed that the transduction efficiency of arginine-rich CPPs can be greatly enhanced by cyclization, the aim was to use cyclic CPPs to transport full-length proteins, in this study green fluorescent protein (GFP), into the cytosol of living cells. Cyclic and linear CPP-GFP conjugates were obtained by using azido-functionalized CPPs and an alkyne-functionalized GFP. Our findings reveal that the cyclic-CPP-GFP conjugates are internalized into live cells with immediate bioavailability in the cytosol and the nucleus, whereas linear CPP analogues do not confer GFP transduction. This technology expands the application of cyclic CPPs to the efficient transport of functional full-length proteins into live cells.
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Affiliation(s)
- Nicole Nischan
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin (Germany); Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, 14195 Berlin (Germany)
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27
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Potocký M, Pleskot R, Pejchar P, Vitale N, Kost B, Žárský V. Live-cell imaging of phosphatidic acid dynamics in pollen tubes visualized by Spo20p-derived biosensor. New Phytol 2014; 203:483-494. [PMID: 24750036 DOI: 10.1111/nph.12814] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 03/14/2014] [Indexed: 05/21/2023]
Abstract
Although phosphatidic acid (PA) is structurally the simplest membrane phospholipid, it has been implicated in the regulation of many cellular events, including cytoskeletal dynamics, membrane trafficking and stress responses. Plant PA shows rapid turnover but the information about its spatio-temporal distribution in plant cells is missing. Here we demonstrate the use of a lipid biosensor that enables us to monitor PA dynamics in plant cells. The biosensor consists of a PA-binding domain of yeast SNARE Spo20p fused to fluorescent proteins. Live-cell imaging of PA dynamics in transiently transformed tobacco (Nicotiana tabacum) pollen tubes was performed using confocal laser scanning microscopy. In growing pollen tubes, PA shows distinct annulus-like fluorescence pattern in the plasma membrane behind the extreme tip. Coexpression studies with markers for other plasmalemma signaling lipids phosphatidylinositol 4,5-bisphosphate and diacylglycerol revealed limited colocalization at the shoulders of the apex. PA distribution and concentrations show distinct responses to various lipid signaling inhibitors. Fluorescence recovery after photobleaching (FRAP) analysis suggests high PA turnover in the plasma membrane. Our data show that a biosensor based on the Spo20p-PA binding domain is suitable for live-cell imaging of PA also in plant cells. In tobacco pollen tubes, distinct subapical PA maximum corroborates its involvement in the regulation of endocytosis and actin dynamics.
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Affiliation(s)
- Martin Potocký
- Institute of Experimental Botany, v. v. i., Academy of Sciences of the Czech Republic, 16502, Prague 6, Czech Republic
| | - Roman Pleskot
- Institute of Experimental Botany, v. v. i., Academy of Sciences of the Czech Republic, 16502, Prague 6, Czech Republic
| | - Přemysl Pejchar
- Institute of Experimental Botany, v. v. i., Academy of Sciences of the Czech Republic, 16502, Prague 6, Czech Republic
| | - Nicolas Vitale
- Institut des Neurosciences Cellulaires et Integratives, CNRS UPR3212 and Université de Strasbourg, Strasbourg, France
| | - Benedikt Kost
- Department of Biology, University of Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Viktor Žárský
- Institute of Experimental Botany, v. v. i., Academy of Sciences of the Czech Republic, 16502, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, 128 44, Prague 2, Czech Republic
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28
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Jonkman JEN, Cathcart JA, Xu F, Bartolini ME, Amon JE, Stevens KM, Colarusso P. An introduction to the wound healing assay using live-cell microscopy. Cell Adh Migr 2014; 8:440-51. [PMID: 25482647 PMCID: PMC5154238 DOI: 10.4161/cam.36224] [Citation(s) in RCA: 359] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 08/17/2014] [Accepted: 08/25/2014] [Indexed: 12/13/2022] Open
Abstract
The wound healing assay is used in a range of disciplines to study the coordinated movement of a cell population. In this technical review, we describe the workflow of the wound healing assay as monitored by optical microscopy. Although the assay is straightforward, a lack of standardization in its application makes it difficult to compare results and reproduce experiments among researchers. We recommend general guidelines for consistency, including: (1) sample preparation including the creation of the gap, (2) microscope equipment requirements, (3) image acquisition, and (4) the use of image analysis to measure the gap size and its rate of closure over time. We also describe parameters that are specific to the particular research question, such as seeding density and matrix coatings. All of these parameters must be carefully controlled within a given set of experiments in order to achieve accurate and reproducible results.
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Affiliation(s)
- James E. N. Jonkman
- Advanced Optical Microscopy Facility;
University Health Network; Toronto, ON Canada
| | - Judith A. Cathcart
- Advanced Optical Microscopy Facility;
University Health Network; Toronto, ON Canada
| | - Feng Xu
- Advanced Optical Microscopy Facility;
University Health Network; Toronto, ON Canada
| | - Miria E. Bartolini
- Advanced Optical Microscopy Facility;
University Health Network; Toronto, ON Canada
| | - Jennifer E. Amon
- Live Cell Imaging Facility; Snyder Institute
for Chronic Diseases; University of Calgary; Calgary, AB
Canada
| | - Katarzyna M. Stevens
- Live Cell Imaging Facility; Snyder Institute
for Chronic Diseases; University of Calgary; Calgary, AB
Canada
| | - Pina Colarusso
- Live Cell Imaging Facility; Snyder Institute
for Chronic Diseases; University of Calgary; Calgary, AB
Canada
- Department of Physiology and Pharmacology;
University of Calgary; Calgary, AB Canada
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29
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Daghma DS, Kumlehn J, Hensel G, Rutten T, Melzer M. Time-lapse imaging of the initiation of pollen embryogenesis in barley (Hordeum vulgare L.). J Exp Bot 2012; 63:6017-21. [PMID: 22991158 PMCID: PMC3467303 DOI: 10.1093/jxb/ers254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Pollen embryogenesis provides exciting opportunities in the areas of breeding and biotechnology as well as representing a convenient model for studying the process of plant cell proliferation in general and embryogenesis in particular. A cell culture system was devised in which immature barley pollen could be cultured as a monolayer trapped between the bottom glass-cover slip of a live-cell chamber and a diaphanous PTFE membrane within a liquid medium over a period of up to 28 d, allowing the process of embryogenesis to be tracked in individual pollen. Z-stacks of images were automatically captured every 3min, starting from the unicellular pollen stage up to the development of multicellular, embryogenic structures. The method should prove useful for the elucidation of ultrastructural features and molecular processes associated with pollen embryogenesis.
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Affiliation(s)
- D. S. Daghma
- Department of Physiology and Cell Biology, Leibniz Institute of
Plant Genetics and Crop Plant Research, D-06466
Gatersleben, Germany
- National Gene Bank and Genetic Resources, Agriculture Research
Center, 12619 Giza, Egypt
| | - J. Kumlehn
- Department of Physiology and Cell Biology, Leibniz Institute of
Plant Genetics and Crop Plant Research, D-06466
Gatersleben, Germany
| | - G. Hensel
- Department of Physiology and Cell Biology, Leibniz Institute of
Plant Genetics and Crop Plant Research, D-06466
Gatersleben, Germany
| | - T. Rutten
- Department of Physiology and Cell Biology, Leibniz Institute of
Plant Genetics and Crop Plant Research, D-06466
Gatersleben, Germany
| | - M. Melzer
- Department of Physiology and Cell Biology, Leibniz Institute of
Plant Genetics and Crop Plant Research, D-06466
Gatersleben, Germany
- To whom correspondence should be addressed: E-mail:
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30
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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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