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Verstraelen P, Van Dyck M, Verschuuren M, Kashikar ND, Nuydens R, Timmermans JP, De Vos WH. Image-Based Profiling of Synaptic Connectivity in Primary Neuronal Cell Culture. Front Neurosci 2018; 12:389. [PMID: 29997468 PMCID: PMC6028601 DOI: 10.3389/fnins.2018.00389] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/22/2018] [Indexed: 12/04/2022] Open
Abstract
Neurological disorders display a broad spectrum of clinical manifestations. Yet, at the cellular level, virtually all these diseases converge into a common phenotype of dysregulated synaptic connectivity. In dementia, synapse dysfunction precedes neurodegeneration and cognitive impairment by several years, making the synapse a crucial entry point for the development of diagnostic and therapeutic strategies. Whereas high-resolution imaging and biochemical fractionations yield detailed insight into the molecular composition of the synapse, standardized assays are required to quickly gauge synaptic connectivity across large populations of cells under a variety of experimental conditions. Such screening capabilities have now become widely accessible with the advent of high-throughput, high-content microscopy. In this review, we discuss how microscopy-based approaches can be used to extract quantitative information about synaptic connectivity in primary neurons with deep coverage. We elaborate on microscopic readouts that may serve as a proxy for morphofunctional connectivity and we critically analyze their merits and limitations. Finally, we allude to the potential of alternative culture paradigms and integrative approaches to enable comprehensive profiling of synaptic connectivity.
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Affiliation(s)
- Peter Verstraelen
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Michiel Van Dyck
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Marlies Verschuuren
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Rony Nuydens
- Janssen Research and Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Jean-Pierre Timmermans
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Winnok H. De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
- Cell Systems and Imaging, Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
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Nozeret K, Loll F, Cardoso GM, Escudé C, Boutorine AS. Interaction of fluorescently labeled pyrrole-imidazole polyamide probes with fixed and living murine and human cells. Biochimie 2018; 149:122-134. [DOI: 10.1016/j.biochi.2018.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 03/14/2018] [Indexed: 12/26/2022]
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Tektonidis M, Rohr K. Diffeomorphic Multi-Frame Non-Rigid Registration of Cell Nuclei in 2D and 3D Live Cell Images. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2017; 26:1405-1417. [PMID: 28092560 DOI: 10.1109/tip.2017.2653360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To gain a better understanding of cellular and molecular processes, it is important to quantitatively analyze the motion of subcellular particles in live cell microscopy image sequences. Since, generally, the subcellular particles move and cell nuclei move as well as deform, it is important to decouple the movement of particles from that of the cell nuclei using non-rigid registration methods. We have developed a diffeomorphic multi-frame approach for non-rigid registration of cell nuclei in 2D and 3D live cell fluorescence microscopy images. Our non-rigid registration approach is based on local optic flow estimation, exploits information from multiple consecutive image frames, and determines diffeomorphic transformations in the log-domain, which allows efficient computation of the inverse transformations. To register single images of an image sequence to a reference image, we use a temporally weighted mean image, which is constructed based on inverse transformations and multiple consecutive frames. Using multiple consecutive frames improves the registration accuracy compared to pairwise registration, and using a temporally weighted mean image significantly reduces the computation time compared with previous work. In addition, we use a flow boundary preserving method for regularization of computed deformation vector fields, which prevents from over-smoothing compared to standard Gaussian filtering. Our approach has been successfully applied to 2D and 3D synthetic as well as real live cell microscopy image sequences, and an experimental comparison with non-rigid pairwise, multi-frame, and temporal groupwise registration has been carried out.
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Nozeret K, Bonan M, Yarmoluk SM, Novopashina DS, Boutorine AS. Synthesis of mouse centromere-targeted polyamides and physico-chemical studies of their interaction with the target double-stranded DNA. Bioorg Med Chem 2015; 23:5932-45. [PMID: 26190459 DOI: 10.1016/j.bmc.2015.06.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 11/18/2022]
Abstract
Synthetic minor groove-binding pyrrole-imidazole polyamides labeled by fluorophores are promising candidates for fluorescence imaging of double-stranded DNA in isolated chromosomes or fixed and living cells. We synthesized nine hairpin and two head-to-head tandem polyamides targeting repeated sequences from mouse major satellites. Their interaction with synthetic target dsDNA has been studied by physico-chemical methods in vitro before and after coupling to various fluorophores. Great variability in affinities and fluorescence properties reveals a conclusion that these properties do not only rely on recognition rules, but also on other known and unknown structural factors. Individual testing of each probe is needed before cellular applications.
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Affiliation(s)
- Karine Nozeret
- Structure and Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris cedex 05, France.
| | - Marc Bonan
- Structure and Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris cedex 05, France; Université Paris René Descartes, 12 Rue de l'École de Médecine, 75006 Paris, France.
| | - Serguiy M Yarmoluk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, ul. Zabolotnogo, 150, P.O. 88, 03187 Kiev, Ukraine.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Lavrentyev prosp., 8, 630090 Novosibirsk, Russia.
| | - Alexandre S Boutorine
- Structure and Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris cedex 05, France.
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Štěpka K, Matula P, Matula P, Wörz S, Rohr K, Kozubek M. Performance and sensitivity evaluation of 3D spot detection methods in confocal microscopy. Cytometry A 2015; 87:759-72. [PMID: 26033916 DOI: 10.1002/cyto.a.22692] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 03/06/2015] [Accepted: 04/30/2015] [Indexed: 12/11/2022]
Abstract
Reliable 3D detection of diffraction-limited spots in fluorescence microscopy images is an important task in subcellular observation. Generally, fluorescence microscopy images are heavily degraded by noise and non-specifically stained background, making reliable detection a challenging task. In this work, we have studied the performance and parameter sensitivity of eight recent methods for 3D spot detection. The study is based on both 3D synthetic image data and 3D real confocal microscopy images. The synthetic images were generated using a simulator modeling the complete imaging setup, including the optical path as well as the image acquisition process. We studied the detection performance and parameter sensitivity under different noise levels and under the influence of uneven background signal. To evaluate the parameter sensitivity, we propose a novel measure based on the gradient magnitude of the F1 score. We measured the success rate of the individual methods for different types of the image data and found that the type of image degradation is an important factor. Using the F1 score and the newly proposed sensitivity measure, we found that the parameter sensitivity is not necessarily proportional to the success rate of a method. This also provided an explanation why the best performing method for synthetic data was outperformed by other methods when applied to the real microscopy images. On the basis of the results obtained, we conclude with the recommendation of the HDome method for data with relatively low variations in quality, or the Sorokin method for image sets in which the quality varies more. We also provide alternative recommendations for high-quality images, and for situations in which detailed parameter tuning might be deemed expensive.
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Affiliation(s)
- Karel Štěpka
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Pavel Matula
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Petr Matula
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Stefan Wörz
- IPMB and BIOQUANT, Department of Bioinformatics and Functional Genomics, and DKFZ, University of Heidelberg, Heidelberg, Germany
| | - Karl Rohr
- IPMB and BIOQUANT, Department of Bioinformatics and Functional Genomics, and DKFZ, University of Heidelberg, Heidelberg, Germany
| | - Michal Kozubek
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
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Nozeret K, Loll F, Escudé C, Boutorine AS. Polyamide fluorescent probes for visualization of repeated DNA sequences in living cells. Chembiochem 2015; 16:549-54. [PMID: 25639955 DOI: 10.1002/cbic.201402676] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Indexed: 11/07/2022]
Abstract
DNA imaging in living cells usually requires transgenic approaches that modify the genome. Synthetic pyrrole-imidazole polyamides that bind specifically to the minor groove of double-stranded DNA (dsDNA) represent an attractive approach for in-cell imaging that does not necessitate changes to the genome. Nine hairpin polyamides that target mouse major satellite DNA were synthesized. Their interactions with synthetic target dsDNA fragments were studied by thermal denaturation, gel-shift electrophoresis, circular dichroism, and fluorescence spectroscopy. The polyamides had different affinities for the target DNA, and fluorescent labeling of the polyamides affected their affinity for their targets. We validated the specificity of the probes in fixed cells and provide evidence that two of the probes detect target sequences in mouse living cell lines. This study demonstrates for the first time that synthetic compounds can be used for the visualization of the nuclear substructures formed by repeated DNA sequences in living cells.
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Affiliation(s)
- Karine Nozeret
- Structure and Instability of Genomes, Sorbonne Universités, Muséum national d'Histoire naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris Cedex 05 (France)
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Girst S, Hable V, Drexler GA, Greubel C, Siebenwirth C, Haum M, Friedl AA, Dollinger G. Subdiffusion supports joining of correct ends during repair of DNA double-strand breaks. Sci Rep 2014; 3:2511. [PMID: 23979012 PMCID: PMC3753591 DOI: 10.1038/srep02511] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/18/2013] [Indexed: 12/03/2022] Open
Abstract
The mobility of damaged chromatin regions in the nucleus may affect the probability of mis-repair. In this work, live-cell observation and distance tracking of GFP-tagged DNA damage response protein MDC1 was used to study the random-walk behaviour of chromatin domains containing radiation-induced DNA double-strand breaks (DSB). Our measurements indicate a subdiffusion-type random walk process with similar time dependence for isolated and clustered DSBs that were induced by 20 MeV proton or 43 MeV carbon ion micro-irradiation. As compared to normal diffusion, subdiffusion enhances the probability that both ends of a DSB meet, thus promoting high efficiency DNA repair. It also limits their probability of long-range movements and thus lowers the probability of mis-rejoining and chromosome aberrations.
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Affiliation(s)
- S Girst
- Angewandte Physik und Messtechnik LRT2, Universität der Bundeswehr München, 85577 Neubiberg, Germany.
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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Londoño-Vallejo JA, Wellinger RJ. Telomeres and telomerase dance to the rhythm of the cell cycle. Trends Biochem Sci 2012; 37:391-9. [PMID: 22727244 DOI: 10.1016/j.tibs.2012.05.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Revised: 05/21/2012] [Accepted: 05/25/2012] [Indexed: 11/27/2022]
Abstract
The stability of the ends of linear eukaryotic chromosomes is ensured by functional telomeres, which are composed of short, species-specific direct repeat sequences. The maintenance of telomeres depends on a specialized ribonucleoprotein (RNP) called telomerase. Both telomeres and telomerase are dynamic entities with different physical behaviors and, given their substrate-enzyme relation, they must establish a productive interaction. Regulatory mechanisms controlling this interaction are key missing elements in our understanding of telomere functions. Here, we review the dynamic properties of telomeres and the maturing telomerase RNPs, and summarize how tracking the timing of their dance during the cell cycle will yield insights into chromosome stability mechanisms. Cancer cells often display loss of genome integrity; therefore, these issues are of particular interest for our understanding of cancer initiation or progression.
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Affiliation(s)
- J Arturo Londoño-Vallejo
- Laboratoire Télomères et Cancer, UMR3244, Institut Curie, 26 rue d'Ulm, 75248 Paris, France; UPMC Université Paris 06, F-75005 Paris, France
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