1
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Schirripa Spagnolo C, Luin S. Impact of temporal resolution in single particle tracking analysis. DISCOVER NANO 2024; 19:87. [PMID: 38724858 PMCID: PMC11082114 DOI: 10.1186/s11671-024-04029-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Temporal resolution is a key parameter in the observation of dynamic processes, as in the case of single molecules motions visualized in real time in two-dimensions by wide field (fluorescence) microscopy, but a systematic investigation of its effects in all the single particle tracking analysis steps is still lacking. Here we present tools to quantify its impact on the estimation of diffusivity and of its distribution using one of the most popular tracking software for biological applications on simulated data and movies. We found important shifts and different widths for diffusivity distributions, depending on the interplay of temporal sampling conditions with various parameters, such as simulated diffusivity, density of spots, signal-to-noise ratio, lengths of trajectories, and kind of boundaries in the simulation. We examined conditions starting from the ones of experiments on the fluorescently labelled receptor p75NTR, a relatively fast-diffusing membrane receptor (diffusivity around 0.5-1 µm2/s), visualized by TIRF microscopy on the basal membrane of living cells. From the analysis of the simulations, we identified the best conditions in cases similar to these ones; considering also the experiments, we could confirm a range of values of temporal resolution suitable for obtaining reliable diffusivity results. The procedure we present can be exploited in different single particle/molecule tracking applications to find an optimal temporal resolution.
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Affiliation(s)
| | - Stefano Luin
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127, Pisa, Italy.
- NEST Laboratory, Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127, Pisa, Italy.
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2
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Ling YH, Ye Z, Liang C, Yu C, Park G, Corden JL, Wu C. Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets. Nat Cell Biol 2024; 26:581-592. [PMID: 38548891 DOI: 10.1038/s41556-024-01382-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/21/2024] [Indexed: 04/09/2024]
Abstract
Efficient gene expression requires RNA polymerase II (RNAPII) to find chromatin targets precisely in space and time. How RNAPII manages this complex diffusive search in three-dimensional nuclear space remains largely unknown. The disordered carboxy-terminal domain (CTD) of RNAPII, which is essential for recruiting transcription-associated proteins, forms phase-separated droplets in vitro, hinting at a potential role in modulating RNAPII dynamics. In the present study, we use single-molecule tracking and spatiotemporal mapping in living yeast to show that the CTD is required for confining RNAPII diffusion within a subnuclear region enriched for active genes, but without apparent phase separation into condensates. Both Mediator and global chromatin organization are required for sustaining RNAPII confinement. Remarkably, truncating the CTD disrupts RNAPII spatial confinement, prolongs target search, diminishes chromatin binding, impairs pre-initiation complex formation and reduces transcription bursting. The present study illuminates the pivotal role of the CTD in driving spatiotemporal confinement of RNAPII for efficient gene expression.
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Affiliation(s)
- Yick Hin Ling
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Ziyang Ye
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Chloe Liang
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Chuofan Yu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Giho Park
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffry L Corden
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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3
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Küçükdogru R, Franz P, Worch R, Robaszkiewicz K, Siatkowska M, Tsiavaliaris G, Moraczewska J. Mechanochemical consequences of myopathy-linked mutations in Tpm2.2 on striated muscle contractility. FASEB J 2024; 38:e23400. [PMID: 38156416 DOI: 10.1096/fj.202301604r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/04/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023]
Abstract
Tropomyosin (Tpm) is an actin-binding protein central to muscle contraction regulation. The Tpm sequence consists of periodic repeats corresponding to seven actin-binding sites, further divided in two functionally distinct halves. To clarify the importance of the first and second halves of the actin-binding periods in regulating the interaction of myosin with actin, we introduced hypercontractile mutations D20H, E181K located in the N-terminal halves of periods 1 and 5 and hypocontractile mutations E41K, N202K located in the C-terminal halves of periods 1 and 5 of the skeletal muscle Tpm isoform Tpm2.2. Wild-type and mutant Tpms displayed similar actin-binding properties, however, as revealed by FRET experiments, the hypercontractile mutations affected the binding geometry and orientation of Tpm2.2 on actin, causing a stimulation of myosin motor performance. Contrary, the hypocontractile mutations led to an inhibition of both, actin activation of the myosin ATPase and motor activity, that was more pronounced than with wild-type Tpm2.2. Single ATP turnover kinetic experiments indicate that the introduced mutations have opposite effects on product release kinetics. While the hypercontractile Tpm2.2 mutants accelerated product release, the hypocontractile mutants decelerated product release from myosin, thus having either an activating or inhibitory influence on myosin motor performance, which agrees with the muscle disease phenotypes caused by these mutations.
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Affiliation(s)
- Recep Küçükdogru
- Department of Biochemistry and Cell Biology, Faculty of Biological Sciences, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Peter Franz
- Cellular Biophysics, Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Remigiusz Worch
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Robaszkiewicz
- Department of Biochemistry and Cell Biology, Faculty of Biological Sciences, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Małgorzata Siatkowska
- Department of Biochemistry and Cell Biology, Faculty of Biological Sciences, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Georgios Tsiavaliaris
- Cellular Biophysics, Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Joanna Moraczewska
- Department of Biochemistry and Cell Biology, Faculty of Biological Sciences, Kazimierz Wielki University, Bydgoszcz, Poland
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4
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Ling YH, Ye Z, Liang C, Yu C, Park G, Corden JL, Wu C. Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551302. [PMID: 37577667 PMCID: PMC10418089 DOI: 10.1101/2023.07.31.551302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Efficient gene expression requires RNA Polymerase II (RNAPII) to find chromatin targets precisely in space and time. How RNAPII manages this complex diffusive search in 3D nuclear space remains largely unknown. The disordered carboxy-terminal domain (CTD) of RNAPII, which is essential for recruiting transcription-associated proteins, forms phase-separated droplets in vitro, hinting at a potential role in modulating RNAPII dynamics. Here, we use single-molecule tracking and spatiotemporal mapping in living yeast to show that the CTD is required for confining RNAPII diffusion within a subnuclear region enriched for active genes, but without apparent phase separation into condensates. Both Mediator and global chromatin organization are required for sustaining RNAPII confinement. Remarkably, truncating the CTD disrupts RNAPII spatial confinement, prolongs target search, diminishes chromatin binding, impairs pre-initiation complex formation, and reduces transcription bursting. This study illuminates the pivotal role of the CTD in driving spatiotemporal confinement of RNAPII for efficient gene expression.
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Affiliation(s)
- Yick Hin Ling
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Ziyang Ye
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Chloe Liang
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Chuofan Yu
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Giho Park
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Jeffry L Corden
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
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5
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Podh NK, Das A, Dey P, Paliwal S, Mehta G. Single-molecule tracking for studying protein dynamics and target-search mechanism in live cells of S. cerevisiae. STAR Protoc 2022; 3:101900. [PMID: 36595957 PMCID: PMC9732415 DOI: 10.1016/j.xpro.2022.101900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/22/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Single-molecule tracking (SMT) is a powerful approach to quantify the biophysical parameters of protein dynamics in live cells. Here, we describe a protocol for SMT in live cells of the budding yeast Saccharomyces cerevisiae. We detail how to genetically engineer yeast strains for SMT, how to set up image acquisition parameters, and how different software programs can be used to quantify a variety of biophysical parameters such as diffusion coefficient, residence time, bound fraction, jump angles, and target-search parameters. For complete details on the use and execution of this protocol, please refer to Mehta et al. 1 and Ball et al..2.
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Affiliation(s)
- Nitesh Kumar Podh
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Ayan Das
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Partha Dey
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Sheetal Paliwal
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Gunjan Mehta
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India,Corresponding author
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6
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Gabriel L, Almeida H, Avelar M, Sarmento B, das Neves J. MPTHub: An Open-Source Software for Characterizing the Transport of Particles in Biorelevant Media. NANOMATERIALS 2022; 12:nano12111899. [PMID: 35683754 PMCID: PMC9182034 DOI: 10.3390/nano12111899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 02/04/2023]
Abstract
The study of particle transport in different environments plays an essential role in understanding interactions with humans and other living organisms. Importantly, obtained data can be directly used for multiple applications in fields such as fundamental biology, toxicology, or medicine. Particle movement in biorelevant media can be readily monitored using microscopy and converted into time-resolved trajectories using freely available tracking software. However, translation into tangible and meaningful parameters is time consuming and not always intuitive. We developed new software—MPTHub—as an open-access, standalone, user-friendly tool for the rapid and reliable analysis of particle trajectories extracted from video microscopy. The software was programmed using Python and allowed to import and analyze trajectory data, as well as to export relevant data such as individual and ensemble time-averaged mean square displacements and effective diffusivity, and anomalous transport exponent. Data processing was reliable, fast (total processing time of less than 10 s), and required minimal memory resources (up to a maximum of around 150 MB in random access memory). Demonstration of software applicability was conducted by studying the transport of different polystyrene nanoparticles (100–200 nm) in mucus surrogates. Overall, MPTHub represents a freely available software tool that can be used even by inexperienced users for studying the transport of particles in biorelevant media.
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Affiliation(s)
- Leandro Gabriel
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (L.G.); (H.A.); (M.A.); (B.S.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- FEUP—Faculdade de Engenharia, Universidade do Porto, 4200-465 Porto, Portugal
| | - Helena Almeida
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (L.G.); (H.A.); (M.A.); (B.S.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Marta Avelar
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (L.G.); (H.A.); (M.A.); (B.S.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- FEUP—Faculdade de Engenharia, Universidade do Porto, 4200-465 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Bruno Sarmento
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (L.G.); (H.A.); (M.A.); (B.S.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- IUCS—Instituto Universitário de Ciências da Saúde, CESPU, 4585-116 Gandra, Portugal
| | - José das Neves
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (L.G.); (H.A.); (M.A.); (B.S.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- IUCS—Instituto Universitário de Ciências da Saúde, CESPU, 4585-116 Gandra, Portugal
- Correspondence: ; Tel.: +351-220-408-800
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7
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Nieves DJ, Pandzic E, Gunasinghe SD, Goyette J, Owen DM, Justin Gooding J, Gaus K. The T cell receptor displays lateral signal propagation involving non-engaged receptors. NANOSCALE 2022; 14:3513-3526. [PMID: 35171177 DOI: 10.1039/d1nr05855j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
T cells are highly sensitive to low levels of antigen, but how this sensitivity is achieved is currently unknown. Here, we imaged proximal TCR-CD3 signal propagation with single molecule localization microscopy (SMLM) in T cells activated with nanoscale clusters of TCR stimuli. We observed the formation of large TCR-CD3 clusters that exceeded the area of the ligand clusters, and required multivalent interactions facilitated by TCR-CD3 phosphorylation for assembly. Within these clustered TCR-CD3 domains, TCR-CD3 signaling spread laterally for ∼500 nm, far beyond the activating site, via non-engaged receptors. Local receptor density determined the functional cooperativity between engaged and non-engaged receptors, but lateral signal propagation was not influenced by the genetic deletion of ZAP70. Taken together, our data demonstrates that clustered ligands induced the clustering of non-ligated TCR-CD3 into domains that cooperatively facilitate lateral signal propagation.
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Affiliation(s)
- Daniel J Nieves
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
- Institute of Immunology and Immunotherapy, School of Mathematics, and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK.
| | - Elvis Pandzic
- Katharina Gaus Light Microscopy Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Sachith D Gunasinghe
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, School of Mathematics, and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK.
| | - J Justin Gooding
- School of Chemistry and Australian Centre for NanoMedicine, University of New South Wales, Sydney, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
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8
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Deep learning detection of nanoparticles and multiple object tracking of their dynamic evolution during in situ ETEM studies. Sci Rep 2022; 12:2484. [PMID: 35169206 PMCID: PMC8847623 DOI: 10.1038/s41598-022-06308-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/24/2022] [Indexed: 11/08/2022] Open
Abstract
In situ transmission electron microscopy (TEM) studies of dynamic events produce large quantities of data especially under the form of images. In the important case of heterogeneous catalysis, environmental TEM (ETEM) under gas and temperature allows to follow a large population of supported nanoparticles (NPs) evolving under reactive conditions. Interpreting properly large image sequences gives precious information on the catalytic properties of the active phase by identifying causes for its deactivation. To perform a quantitative, objective and robust treatment, we propose an automatic procedure to track nanoparticles observed in Scanning ETEM (STEM in ETEM). Our approach involves deep learning and computer vision developments in multiple object tracking. At first, a registration step corrects the image displacements and misalignment inherent to the in situ acquisition. Then, a deep learning approach detects the nanoparticles on all frames of video sequences. Finally, an iterative tracking algorithm reconstructs their trajectories. This treatment allows to deduce quantitative and statistical features about their evolution or motion, such as a Brownian behavior and merging or crossing events. We treat the case of in situ calcination of palladium (oxide) / delta-alumina, where the present approach allows a discussion of operating processes such as Ostwald ripening or NP aggregative coalescence.
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Application of Rapid Fluorescence Lifetime Imaging Microscopy (RapidFLIM) to Examine Dynamics of Nanoparticle Uptake in Live Cells. Cells 2022; 11:cells11040642. [PMID: 35203292 PMCID: PMC8870300 DOI: 10.3390/cells11040642] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/28/2022] [Accepted: 02/09/2022] [Indexed: 02/01/2023] Open
Abstract
A key challenge in nanomedicine stems from the continued need for a systematic understanding of the delivery of nanoparticles in live cells. Complexities in delivery are often influenced by the biophysical characteristics of nanoparticles, where even subtle changes to nanoparticle designs can alter cellular uptake, transport and activity. Close examination of these processes, especially with imaging, offers important insights that can aid in future nanoparticle design or translation. Rapid fluorescence lifetime imaging microscopy (RapidFLIM) is a potentially valuable technology for examining intracellular mechanisms of nanoparticle delivery by directly correlating visual data with changes in the biological environment. To date, applications for this technology in nanoparticle research have not been explored. A PicoQuant RapidFLIM system was used together with commercial silica nanoparticles to follow particle uptake in glioblastoma cells. Importantly, RapidFLIM imaging showed significantly improved image acquisition speeds over traditional FLIM, which enabled the tracking of nanoparticle uptake into subcellular compartments. We determined mean lifetime changes and used this to delineate significant changes in nanoparticle lifetimes (>0.39 ns), which showed clustering of these tracks proximal to both extracellular and nuclear membrane boundaries. These findings demonstrate the ability of RapidFLIM to track, localize and quantify changes in single nanoparticle fluorescence lifetimes and highlight RapidFLIM as a valuable tool for multiparameter visualization and analysis of nanoparticle molecular dynamics in live cells.
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10
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Cheng HJ, Hsu CH, Hung CL, Lin CY. A review for Cell and Particle Tracking on Microscopy Images using Algorithms and Deep Learning Technologies. Biomed J 2021; 45:465-471. [PMID: 34628059 PMCID: PMC9421944 DOI: 10.1016/j.bj.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 01/06/2023] Open
Abstract
Time-lapse microscopy images generated by biological experiments have been widely used for observing target activities, such as the motion trajectories and survival states. Based on these observations, biologists can conclude experimental results or present new hypotheses for several biological applications, i.e. virus research or drug design. Many methods or tools have been proposed in the past to observe cell and particle activities, which are defined as single cell tracking and single particle tracking problems, by using algorithms and deep learning technologies. In this article, a review for these works is presented in order to summarize the past methods and research topics at first, then points out the problems raised by these works, and finally proposes future research directions. The contributions of this article will help researchers to understand past development trends and further propose innovative technologies.
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Affiliation(s)
- Hui-Jun Cheng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China; Department of Computer Science and Information Engineering, Providence University, Taichung 43301, Taiwan
| | - Ching-Hsien Hsu
- Department of Computer Science and Information Engineering, Asia University, Taichung 41354, Taiwan; Guangdong-Hong Kong-Macao Joint Laboratory for Intelligent Micro-Nano Optoelectronic Technology, School of Mathematics and Big Data, Foshan University, Foshan 528000, China; Department of Medical Research, China Medical University Hospital, China Medical University, Taiwan
| | - Che-Lun Hung
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; Department of Computer Science and Communication Engineering, Providence University, Taichung 43301, Taiwan
| | - Chun-Yuan Lin
- Department of Computer Science and Information Engineering, Asia University, Taichung 41354, Taiwan; Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan 33302, Taiwan.
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11
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Basyuk E, Rage F, Bertrand E. RNA transport from transcription to localized translation: a single molecule perspective. RNA Biol 2021; 18:1221-1237. [PMID: 33111627 PMCID: PMC8354613 DOI: 10.1080/15476286.2020.1842631] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/21/2022] Open
Abstract
Transport of mRNAs is an important step of gene expression, which brings the genetic message from the DNA in the nucleus to a precise cytoplasmic location in a regulated fashion. Perturbation of this process can lead to pathologies such as developmental and neurological disorders. In this review, we discuss recent advances in the field of mRNA transport made using single molecule fluorescent imaging approaches. We present an overview of these approaches in fixed and live cells and their input in understanding the key steps of mRNA journey: transport across the nucleoplasm, export through the nuclear pores and delivery to its final cytoplasmic location. This review puts a particular emphasis on the coupling of mRNA transport with translation, such as localization-dependent translational regulation and translation-dependent mRNA localization. We also highlight the recently discovered translation factories, and how cellular and viral RNAs can hijack membrane transport systems to travel in the cytoplasm.
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Affiliation(s)
- Eugenia Basyuk
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Present address: Laboratoire de Microbiologie Fondamentale et Pathogénicité, CNRS-UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Florence Rage
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
- Equipe Labélisée Ligue Nationale Contre Le Cancer, Montpellier, France
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12
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Pertici I, Taft MH, Greve JN, Fedorov R, Caremani M, Manstein DJ. Allosteric modulation of cardiac myosin mechanics and kinetics by the conjugated omega-7,9 trans-fat rumenic acid. J Physiol 2021; 599:3639-3661. [PMID: 33942907 DOI: 10.1113/jp281563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/28/2021] [Indexed: 01/23/2023] Open
Abstract
KEY POINTS Direct binding of rumenic acid to the cardiac myosin-2 motor domain increases the release rate for orthophosphate and increases the Ca2+ responsiveness of cardiac muscle at low load. Physiological cellular concentrations of rumenic acid affect the ATP turnover rates of the super-relaxed and disordered relaxed states of β-cardiac myosin, leading to a net increase in myocardial metabolic load. In Ca2+ -activated trabeculae, rumenic acid exerts a direct inhibitory effect on the force-generating mechanism without affecting the number of force-generating motors. In the presence of saturating actin concentrations rumenic acid binds to the β-cardiac myosin-2 motor domain with an EC50 of 200 nM. Molecular docking studies provide information about the binding site, the mode of binding, and associated allosteric communication pathways. Free rumenic acid may exceed thresholds in cardiomyocytes above which contractile efficiency is reduced and interference with small molecule therapeutics, targeting cardiac myosin, occurs. ABSTRACT Based on experiments using purified myosin motor domains, reconstituted actomyosin complexes and rat heart ventricular trabeculae, we demonstrate direct binding of rumenic acid, the cis-delta-9-trans-delta-11 isomer of conjugated linoleic acid, to an allosteric site located in motor domain of mammalian cardiac myosin-2 isoforms. In the case of porcine β-cardiac myosin, the EC50 for rumenic acid varies from 10.5 μM in the absence of actin to 200 nM in the presence of saturating concentrations of actin. Saturating concentrations of rumenic acid increase the maximum turnover of basal and actin-activated ATPase activity of β-cardiac myosin approximately 2-fold but decrease the force output per motor by 23% during isometric contraction. The increase in ATP turnover is linked to an acceleration of the release of the hydrolysis product orthophosphate. In the presence of 5 μM rumenic acid, the difference in the rate of ATP turnover by the super-relaxed and disordered relaxed states of cardiac myosin increases from 4-fold to 20-fold. The equilibrium between the two functional myosin states is not affected by rumenic acid. Calcium responsiveness is increased under zero-load conditions but unchanged under load. Molecular docking studies provide information about the rumenic acid binding site, the mode of binding, and associated allosteric communication pathways. They show how the isoform-specific replacement of residues in the binding cleft induces a different mode of rumenic acid binding in the case of non-muscle myosin-2C and blocks binding to skeletal muscle and smooth muscle myosin-2 isoforms.
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Affiliation(s)
- Irene Pertici
- PhysioLab, University of Florence, Florence, 50019, Italy.,Institute for Biophysical Chemistry, OE4350, Medizinische Hochschule Hannover, Hannover, 30625, Germany
| | - Manuel H Taft
- Institute for Biophysical Chemistry, OE4350, Medizinische Hochschule Hannover, Hannover, 30625, Germany
| | - Johannes N Greve
- Institute for Biophysical Chemistry, OE4350, Medizinische Hochschule Hannover, Hannover, 30625, Germany
| | - Roman Fedorov
- Division of Structural Biochemistry, OE8830, Medizinische Hochschule Hannover, Hannover, 30625, Germany.,RESiST, Cluster of Excellence 2155, Medizinische Hochschule Hannover, Hannover, 30625, Germany
| | - Marco Caremani
- PhysioLab, University of Florence, Florence, 50019, Italy
| | - Dietmar J Manstein
- Institute for Biophysical Chemistry, OE4350, Medizinische Hochschule Hannover, Hannover, 30625, Germany.,Division of Structural Biochemistry, OE8830, Medizinische Hochschule Hannover, Hannover, 30625, Germany.,RESiST, Cluster of Excellence 2155, Medizinische Hochschule Hannover, Hannover, 30625, Germany
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13
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Kuhn T, Hettich J, Davtyan R, Gebhardt JCM. Single molecule tracking and analysis framework including theory-predicted parameter settings. Sci Rep 2021; 11:9465. [PMID: 33947895 PMCID: PMC8096815 DOI: 10.1038/s41598-021-88802-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/16/2021] [Indexed: 02/02/2023] Open
Abstract
Imaging, tracking and analyzing individual biomolecules in living systems is a powerful technology to obtain quantitative kinetic and spatial information such as reaction rates, diffusion coefficients and localization maps. Common tracking tools often operate on single movies and require additional manual steps to analyze whole data sets or to compare different experimental conditions. We report a fast and comprehensive single molecule tracking and analysis framework (TrackIt) to simultaneously process several multi-movie data sets. A user-friendly GUI offers convenient tracking visualization, multiple state-of-the-art analysis procedures, display of results, and data im- and export at different levels to utilize external software tools. We applied our framework to quantify dissociation rates of a transcription factor in the nucleus and found that tracking errors, similar to fluorophore photobleaching, have to be considered for reliable analysis. Accordingly, we developed an algorithm, which accounts for both tracking losses and suggests optimized tracking parameters when evaluating reaction rates. Our versatile and extensible framework facilitates quantitative analysis of single molecule experiments at different experimental conditions.
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Affiliation(s)
- Timo Kuhn
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Johannes Hettich
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Rubina Davtyan
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany ,grid.4514.40000 0001 0930 2361Present Address: NanoLund and Solid State Physics, Lund University, Box 118, 22100 Lund, Sweden
| | - J. Christof M. Gebhardt
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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14
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Eördögh Á, Paganini C, Pinotsi D, Arosio P, Rivera-Fuentes P. A Molecular Logic Gate Enables Single-Molecule Imaging and Tracking of Lipids in Intracellular Domains. ACS Chem Biol 2020; 15:2597-2604. [PMID: 32803945 DOI: 10.1021/acschembio.0c00639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Photoactivatable dyes enable single-molecule imaging and tracking in biology. Despite progress in the development of new fluorophores and labeling strategies, many intracellular compartments remain difficult to image beyond the limit of diffraction in living cells. For example, lipid domains, e.g., membranes and droplets, remain difficult to image with nanometric resolution. To visualize these challenging subcellular targets, it is necessary to develop new fluorescent molecular devices beyond simple on/off switches. Here, we report a fluorogenic molecular logic gate that can be used to image single molecules associated with lipid domains, most notably droplets, with excellent specificity. This probe requires the subsequent action of light, a lipophilic environment, and a competent nucleophile to produce a fluorescent product. The combination of these inputs results in a probe that can be used to image the boundary of lipid droplets in three dimensions with resolution beyond the limit of diffraction. Moreover, this probe enables single-molecule tracking of lipid trafficking between droplets and the endoplasmic reticulum.
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Affiliation(s)
- Ádám Eördögh
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
- Institute of Chemical Sciences and Engineering, EPF Lausanne, 1015 Lausanne, Switzerland
| | - Carolina Paganini
- Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, 8093 Zurich, Switzerland
| | - Paolo Arosio
- Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Pablo Rivera-Fuentes
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
- Institute of Chemical Sciences and Engineering, EPF Lausanne, 1015 Lausanne, Switzerland
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15
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Jin L, Zhao F, Lin W, Zhou X, Kuang C, Nedzved A, Ablameyko S, Liu X, Xu Y. Development of fan‐shaped tracker for single particle tracking. Microsc Res Tech 2020; 83:1056-1065. [DOI: 10.1002/jemt.23496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/11/2020] [Accepted: 03/29/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Luhong Jin
- Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio‐Cerebral Vascular Detection Technology and Medicinal Effectiveness AppraisalZhejiang University Hangzhou 310027 China
| | - Fengqiang Zhao
- Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio‐Cerebral Vascular Detection Technology and Medicinal Effectiveness AppraisalZhejiang University Hangzhou 310027 China
| | - Wanni Lin
- Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio‐Cerebral Vascular Detection Technology and Medicinal Effectiveness AppraisalZhejiang University Hangzhou 310027 China
| | - Xiaoxu Zhou
- Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio‐Cerebral Vascular Detection Technology and Medicinal Effectiveness AppraisalZhejiang University Hangzhou 310027 China
| | - Cuifang Kuang
- State Key Laboratory of Modern Optical Instrumentation, Department of Optical EngineeringZhejiang University Hangzhou 310027 China
| | - Alexander Nedzved
- National Academy of Sciences, United Institute of Informatics ProblemsBelarusian State University Minsk 220012 Republic of Belarus
| | - Sergey Ablameyko
- National Academy of Sciences, United Institute of Informatics ProblemsBelarusian State University Minsk 220012 Republic of Belarus
| | - Xu Liu
- State Key Laboratory of Modern Optical Instrumentation, Department of Optical EngineeringZhejiang University Hangzhou 310027 China
| | - Yingke Xu
- Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio‐Cerebral Vascular Detection Technology and Medicinal Effectiveness AppraisalZhejiang University Hangzhou 310027 China
- Department of Endocrinology, The Affiliated Sir Run Shaw HospitalZhejiang University School of Medicine Hangzhou 310016 China
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16
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Chan JS, Poh PE, Ismadi MZP, Yeo LY, Tan MK. Enhancing greywater treatment via MHz-Order surface acoustic waves. WATER RESEARCH 2020; 169:115187. [PMID: 31671294 DOI: 10.1016/j.watres.2019.115187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/04/2019] [Accepted: 10/12/2019] [Indexed: 06/10/2023]
Abstract
There is a pressing need for efficient biological treatment systems for the removal of organic compounds in greywater given the rapid increase in household wastewater produced as a consequence of rapid urbanisation. Moreover, proper treatment of greywater allows its reuse that can significantly reduce the demand for freshwater supplies. Herein, we demonstrate the possibility of enhancing the removal efficiency of solid contaminants from greywater using MHz-order surface acoustic waves (SAWs). A key distinction of the use of these high frequency surface acoustic waves, compared to previous work on its lower frequency (kHz order) bulk ultrasound counterpart for wastewater treatment, is the absence of cavitation, which can inflict considerable damage on bacteria, thus limiting the intensity and duration, and hence the efficiency enhancement, associated with the acoustic exposure. In particular, we show that up to fivefold improvement in the removal efficiency can be obtained, primarily due to the ability of the acoustic pressure field in homogenizing and reducing the size of bacterial clusters in the sample, therefore providing a larger surface area that promotes greater bacteria digestion. Alternatively, the SAW exposure allows the reduction in the treatment duration to achieve a given level of removal efficiency, thus facilitating higher treatment rates and hence processing throughput. Given the low-cost of the miniature chipscale platform, these promising results highlight its possibility for portable greywater treatment for domestic use or for large-scale industrial wastewater processing through massive parallelization.
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Affiliation(s)
- Jing S Chan
- School of Engineering, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | - Phaik E Poh
- School of Engineering, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | - Mohd-Zulhilmi P Ismadi
- School of Engineering, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | - Leslie Y Yeo
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, VIC, 3001, Australia
| | - Ming K Tan
- School of Engineering, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia.
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17
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Kim D, Rashid F, Cho Y, Zaher MS, Cho IIH, Hamdan SM, Jeong C, Lee JB. DNA skybridge: 3D structure producing a light sheet for high-throughput single-molecule imaging. Nucleic Acids Res 2019; 47:e107. [PMID: 31340015 PMCID: PMC6765118 DOI: 10.1093/nar/gkz625] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/01/2019] [Accepted: 07/12/2019] [Indexed: 11/14/2022] Open
Abstract
Real-time visualization of single-proteins or -complexes on nucleic acid substrates is an essential tool for characterizing nucleic acid binding proteins. Here, we present a novel surface-condition independent and high-throughput single-molecule optical imaging platform called ‘DNA skybridge’. The DNA skybridge is constructed in a 3D structure with 4 μm-high thin quartz barriers in a quartz slide. Each DNA end is attached to the top of the adjacent barrier, resulting in the extension and immobilization of DNA. In this 3D structure, the bottom surface is out-of-focus when the target molecules on the DNA are imaged. Moreover, the DNA skybridge itself creates a thin Gaussian light sheet beam parallel to the immobilized DNA. This dual property allows for imaging a single probe-tagged molecule moving on DNA while effectively suppressing interference with the surface and background signals from the surface.
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Affiliation(s)
- Daehyung Kim
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Fahad Rashid
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Yeonmo Cho
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Manal S Zaher
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - I I Hwan Cho
- Department of Electronic Engineering, Myongji University, Yongin, Gyeonggi 17058, Korea
| | - Samir M Hamdan
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Cherlhyun Jeong
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Korea
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea.,School of Interdisciplinary of Bioscience & Bioengineering, POSTECH, Pohang 37673, Korea
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18
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Wong KS, Lee L, Hung YM, Yeo LY, Tan MK. Lamb to Rayleigh Wave Conversion on Superstrates as a Means to Facilitate Disposable Acoustomicrofluidic Applications. Anal Chem 2019; 91:12358-12368. [DOI: 10.1021/acs.analchem.9b02850] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kiing S. Wong
- School of Engineering, Monash University Malaysia, 47500 Bandar Sunway, Selangor Malaysia
| | - Lillian Lee
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, Victoria 3001, Australia
| | - Yew M. Hung
- School of Engineering, Monash University Malaysia, 47500 Bandar Sunway, Selangor Malaysia
| | - Leslie Y. Yeo
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, Victoria 3001, Australia
| | - Ming K. Tan
- School of Engineering, Monash University Malaysia, 47500 Bandar Sunway, Selangor Malaysia
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19
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DEAD-box ATPases are global regulators of phase-separated organelles. Nature 2019; 573:144-148. [DOI: 10.1038/s41586-019-1502-y] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/19/2019] [Indexed: 12/20/2022]
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20
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Lim E, Lee L, Yeo LY, Hung YM, Tan MK. Acoustically Driven Micromixing: Effect of Transducer Geometry. IEEE TRANSACTIONS ON ULTRASONICS, FERROELECTRICS, AND FREQUENCY CONTROL 2019; 66:1387-1394. [PMID: 31180889 DOI: 10.1109/tuffc.2019.2920683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The ability to drive efficient micromixing on a microfluidic platform is crucial for a wide range of lab-on-a-chip applications. Here, we investigate the ability of acoustic waves generated on different geometric surfaces (concave and convex) to enhance the micromixing efficiency in droplet acoustomicrofluidic systems, and, concomitantly, to reduce the power consumption in these devices for a given performance requirement. Quite counterintuitively, we observe that although the acoustic streaming velocity, which scaled inversely with the droplet size, tended to be generally lower (by approximately 45%) when the flow is generated by transducers with convex surfaces compared to those with concave surfaces, the mixing efficiency is disproportionately higher: compared to pure diffusional mixing in the absence of the acoustic forcing, the mixing efficiency due to the acoustically driven convection increased by up to 25% and 43% on these respective surfaces. As such, the mixing enhancement cannot simply be attributed to an increase in the convective flow arising from the acoustic forcing. Rather, we observe the mixing enhancement to be due to the stronger chaotic advection arising in the transducer with the convex surface due to its diverging acoustic field into the droplet.
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21
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Pamula MC, Carlini L, Forth S, Verma P, Suresh S, Legant WR, Khodjakov A, Betzig E, Kapoor TM. High-resolution imaging reveals how the spindle midzone impacts chromosome movement. J Cell Biol 2019; 218:2529-2544. [PMID: 31248912 PMCID: PMC6683753 DOI: 10.1083/jcb.201904169] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/21/2019] [Accepted: 05/30/2019] [Indexed: 12/11/2022] Open
Abstract
Microtubule bundles in the spindle midzone have been reported to either promote or hinder chromosome movement. Pamula et al. examine the assembly dynamics of midzone microtubule bundles during anaphase and how chromosome segregation is impacted by aberrant bundle assembly. In the spindle midzone, microtubules from opposite half-spindles form bundles between segregating chromosomes. Microtubule bundles can either push or restrict chromosome movement during anaphase in different cellular contexts, but how these activities are achieved remains poorly understood. Here, we use high-resolution live-cell imaging to analyze individual microtubule bundles, growing filaments, and chromosome movement in dividing human cells. Within bundles, filament overlap length marked by the cross-linking protein PRC1 decreases during anaphase as chromosome segregation slows. Filament ends within microtubule bundles appear capped despite dynamic PRC1 turnover and submicrometer proximity to growing microtubules. Chromosome segregation distance and rate are increased in two human cell lines when microtubule bundle assembly is prevented via PRC1 knockdown. Upon expressing a mutant PRC1 with reduced microtubule affinity, bundles assemble but chromosome hypersegregation is still observed. We propose that microtubule overlap length reduction, typically linked to pushing forces generated within filament bundles, is needed to properly restrict spindle elongation and position chromosomes within daughter cells.
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Affiliation(s)
- Melissa C Pamula
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY
| | - Lina Carlini
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY
| | - Scott Forth
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY
| | - Priyanka Verma
- Department of Cancer Biology, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Subbulakshmi Suresh
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY
| | - Wesley R Legant
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC.,Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, and North Carolina State University, Raleigh, NC
| | - Alexey Khodjakov
- Wadsworth Center, New York State Department of Health, Albany, NY
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA.,Department of Physics and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY
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22
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Moroshkin P, Leiderer P, Kono K, Inui S, Tsubota M. Dynamics of the Vortex-Particle Complexes Bound to the Free Surface of Superfluid Helium. PHYSICAL REVIEW LETTERS 2019; 122:174502. [PMID: 31107083 DOI: 10.1103/physrevlett.122.174502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 02/24/2019] [Indexed: 06/09/2023]
Abstract
We present an experimental and theoretical study of the 2D dynamics of electrically charged nanoparticles trapped under a free surface of superfluid helium in a static vertical electric field. We focus on the dynamics of particles driven by the interaction with quantized vortices terminating at the free surface. We identify two types of particle trajectories and the associated vortex structures: vertical linear vortices pinned at the bottom of the container and half-ring vortices traveling along the free surface of the liquid.
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Affiliation(s)
- P Moroshkin
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, 351-0198 Saitama, Japan
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, 904-0495 Okinawa, Japan
| | - P Leiderer
- Department of Physics, University of Konstanz, Universitätstrasse 10, 78464 Konstanz, Germany
| | - K Kono
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, 351-0198 Saitama, Japan
- International College of Semiconductor Technology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - S Inui
- Department of Physics, Osaka City University, 3-3-138 Sugimoto, 558-8585 Osaka, Japan
| | - M Tsubota
- Department of Physics, Osaka City University, 3-3-138 Sugimoto, 558-8585 Osaka, Japan
- Nambu Yoichiro Institute of Theoretical and Experimental Physics, The Advanced Research Institute for Natural Science and Technology, Osaka City University, 3-3-138 Sugimoto, 558-8585 Osaka, Japan
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23
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Bopp N, Scheid LM, Fink RHA, Rohr K. Determination of the Maximum Velocity of Filaments in the in vitro Motility Assay. Front Physiol 2019; 10:289. [PMID: 30971940 PMCID: PMC6445948 DOI: 10.3389/fphys.2019.00289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 03/05/2019] [Indexed: 11/13/2022] Open
Abstract
The in vitro motility assay (IVMA) is a powerful tool commonly used in basic muscle research and for drug screenings with the aim to find treatment options for neuromuscular disorders. In brief, the sliding movement of fluorescence-labeled actin filaments on myosin motor proteins is recorded, and the sliding velocity is analyzed via image analysis methods. Due to low signal-to-noise ratios and large variability in the velocity signal, accurate determination of the maximum sliding velocity is challenging. We introduce a new method and software program named Actin Phase Velocity (ActiPHV). The method extracts the maximum velocity from filament tracking data. Based on simulated and real reference data we show that our method yields a higher accuracy compared to previous methods. As a result, our method enables enhancing the sensitivity of the IVMA to better exploit its full potential.
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Affiliation(s)
- Nasrin Bopp
- Biomedical Computer Vision Group, BioQuant Center and IPMB, University of Heidelberg and DKFZ, Heidelberg, Germany.,Medical Biophysics Unit, Medical Faculty, Institute for Physiology und Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - Lisa-Mareike Scheid
- Medical Biophysics Unit, Medical Faculty, Institute for Physiology und Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - Rainer H A Fink
- Medical Biophysics Unit, Medical Faculty, Institute for Physiology und Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant Center and IPMB, University of Heidelberg and DKFZ, Heidelberg, Germany
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24
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Sachdev R, Hondele M, Linsenmeier M, Vallotton P, Mugler CF, Arosio P, Weis K. Pat1 promotes processing body assembly by enhancing the phase separation of the DEAD-box ATPase Dhh1 and RNA. eLife 2019; 8:41415. [PMID: 30648970 PMCID: PMC6366900 DOI: 10.7554/elife.41415] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/15/2019] [Indexed: 12/24/2022] Open
Abstract
Processing bodies (PBs) are cytoplasmic mRNP granules that assemble via liquid-liquid phase separation and are implicated in the decay or storage of mRNAs. How PB assembly is regulated in cells remains unclear. Previously, we identified the ATPase activity of the DEAD-box protein Dhh1 as a key regulator of PB dynamics and demonstrated that Not1, an activator of the Dhh1 ATPase and member of the CCR4-NOT deadenylase complex inhibits PB assembly in vivo (Mugler et al., 2016). Here, we show that the PB component Pat1 antagonizes Not1 and promotes PB assembly via its direct interaction with Dhh1. Intriguingly, in vivo PB dynamics can be recapitulated in vitro, since Pat1 enhances the phase separation of Dhh1 and RNA into liquid droplets, whereas Not1 reverses Pat1-Dhh1-RNA condensation. Overall, our results uncover a function of Pat1 in promoting the multimerization of Dhh1 on mRNA, thereby aiding the assembly of large multivalent mRNP granules that are PBs.
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Affiliation(s)
| | | | | | | | - Christopher F Mugler
- ETH Zurich, Zurich, Switzerland.,University of California, Berkeley, Berkeley, United States
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25
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Rösch TC, Oviedo-Bocanegra LM, Fritz G, Graumann PL. SMTracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of B. subtilis global repressor AbrB throughout the genome. Sci Rep 2018; 8:15747. [PMID: 30356068 PMCID: PMC6200787 DOI: 10.1038/s41598-018-33842-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/02/2018] [Indexed: 01/08/2023] Open
Abstract
Single-particle (molecule) tracking (SPT/SMT) is a powerful method to study dynamic processes in living cells at high spatial and temporal resolution. Even though SMT is becoming a widely used method in bacterial cell biology, there is no program employing different analytical tools for the quantitative evaluation of tracking data. We developed SMTracker, a MATLAB-based graphical user interface (GUI) for automatically quantifying, visualizing and managing SMT data via five interactive panels, allowing the user to interactively explore tracking data from several conditions, movies and cells on a track-by-track basis. Diffusion constants are calculated a) by a Gaussian mixture model (GMM) panel, analyzing the distribution of positional displacements in x- and y-direction using a multi-state diffusion model (e.g. DNA-bound vs. freely diffusing molecules), and inferring the diffusion constants and relative fraction of molecules in each state, or b) by square displacement analysis (SQD), using the cumulative probability distribution of square displacements to estimate the diffusion constants and relative fractions of up to three diffusive states, or c) through mean-squared displacement (MSD) analyses, allowing the discrimination between Brownian, sub- or superdiffusive behavior. A spatial distribution analysis (SDA) panel analyzes the subcellular localization of molecules, summarizing the localization of trajectories in 2D- heat maps. Using SMTracker, we show that the global transcriptional repressor AbrB performs highly dynamic binding throughout the Bacillus subtilis genome, with short dwell times that indicate high on/off rates in vivo. While about a third of AbrB molecules are in a DNA-bound state, 40% diffuse through the chromosome, and the remaining molecules freely diffuse through the cells. AbrB also forms one or two regions of high intensity binding on the nucleoids, similar to the global gene silencer H-NS in Escherichia coli, indicating that AbrB may also confer a structural function in genome organization.
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Affiliation(s)
- Thomas C Rösch
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Luis M Oviedo-Bocanegra
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Georg Fritz
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany. .,Department of Physics, Philipps Universität Marburg, Marburg, Germany.
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany. .,Department of Chemistry, Philipps Universität Marburg, Marburg, Germany.
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26
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Landvogt L, Ruland JA, Montellese C, Siebrasse JP, Kutay U, Kubitscheck U. Observing and tracking single small ribosomal subunits in vivo. Methods 2018; 153:63-70. [PMID: 30194975 DOI: 10.1016/j.ymeth.2018.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 12/15/2022] Open
Abstract
Ribosomes are formed of a small and a large subunit (SSU/LSU), both consisting of rRNA and a plethora of accessory proteins. While biochemical and genetic studies identified most of the involved proteins and deciphered the ribosomal synthesis steps, our knowledge of the molecular dynamics of the different ribosomal subunits and also of the kinetics of their intracellular trafficking is still limited. Adopting a labelling strategy initially used to study mRNA export we were able to fluorescently stain the SSU in vivo. We chose DIM2/PNO1 (Defective In DNA Methylation 2/Partner of NOb1) as labelling target and created a stable cell line carrying an inducible SNAP-DIM2 fusion protein. After bulk labelling with a green fluorescent dye combined with very sparse labelling with a red fluorescent dye the nucleoli and single SSU could be visualized simultaneously in the green and red channel, respectively. We used single molecule microscopy to track single SSU in the nucleolus and nucleoplasm. Resulting trajectory data were analyzed by jump-distance analysis and the variational Bayes single-particle tracking approach. Both methods allowed identifying the number of diffusive states and the corresponding diffusion coefficients. For both nucleoli and nucleoplasm we could identify mobile (D = 2.3-2.8 µm2/s), retarded (D = 0.18-0.31 µm2/s) and immobilized (D = 0.04-0.05 µm2/s) SSU fractions and, as expected, the size of the fractions differed in the two compartments. While the fast mobility fraction matches perfectly the expected nuclear mobility of the SSU (D = 2.45 µm2/s), we were surprised to find a substantial fraction (33%) of immobile SSU in the nucleoplasm, something not observed for inert control molecules.
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Affiliation(s)
- Lisa Landvogt
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, 53115 Bonn, Germany
| | - Jan Andreas Ruland
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, 53115 Bonn, Germany
| | - Christian Montellese
- Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Jan Peter Siebrasse
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, 53115 Bonn, Germany
| | - Ulrike Kutay
- Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, 53115 Bonn, Germany.
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Dultz E, Mancini R, Polles G, Vallotton P, Alber F, Weis K. Quantitative imaging of chromatin decompaction in living cells. Mol Biol Cell 2018; 29:1763-1777. [PMID: 29771637 DOI: 10.1101/219253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Chromatin organization is highly dynamic and regulates transcription. Upon transcriptional activation, chromatin is remodeled and referred to as "open," but quantitative and dynamic data of this decompaction process are lacking. Here, we have developed a quantitative high resolution-microscopy assay in living yeast cells to visualize and quantify chromatin dynamics using the GAL7-10-1 locus as a model system. Upon transcriptional activation of these three clustered genes, we detect an increase of the mean distance across this locus by >100 nm. This decompaction is linked to active transcription but is not sensitive to the histone deacetylase inhibitor trichostatin A or to deletion of the histone acetyl transferase Gcn5. In contrast, the deletion of SNF2 (encoding the ATPase of the SWI/SNF chromatin remodeling complex) or the deactivation of the histone chaperone complex FACT lead to a strongly reduced decompaction without significant effects on transcriptional induction in FACT mutants. Our findings are consistent with nucleosome remodeling and eviction activities being major contributors to chromatin reorganization during transcription but also suggest that transcription can occur in the absence of detectable decompaction.
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Affiliation(s)
- Elisa Dultz
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Roberta Mancini
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Guido Polles
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Pascal Vallotton
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Frank Alber
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Karsten Weis
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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28
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Dultz E, Mancini R, Polles G, Vallotton P, Alber F, Weis K. Quantitative imaging of chromatin decompaction in living cells. Mol Biol Cell 2018; 29:1763-1777. [PMID: 29771637 PMCID: PMC6080713 DOI: 10.1091/mbc.e17-11-0648] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chromatin organization is highly dynamic and regulates transcription. Upon transcriptional activation, chromatin is remodeled and referred to as “open,” but quantitative and dynamic data of this decompaction process are lacking. Here, we have developed a quantitative high resolution–microscopy assay in living yeast cells to visualize and quantify chromatin dynamics using the GAL7-10-1 locus as a model system. Upon transcriptional activation of these three clustered genes, we detect an increase of the mean distance across this locus by >100 nm. This decompaction is linked to active transcription but is not sensitive to the histone deacetylase inhibitor trichostatin A or to deletion of the histone acetyl transferase Gcn5. In contrast, the deletion of SNF2 (encoding the ATPase of the SWI/SNF chromatin remodeling complex) or the deactivation of the histone chaperone complex FACT lead to a strongly reduced decompaction without significant effects on transcriptional induction in FACT mutants. Our findings are consistent with nucleosome remodeling and eviction activities being major contributors to chromatin reorganization during transcription but also suggest that transcription can occur in the absence of detectable decompaction.
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Affiliation(s)
- Elisa Dultz
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Roberta Mancini
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Guido Polles
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Pascal Vallotton
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Frank Alber
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Karsten Weis
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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29
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Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy. Proc Natl Acad Sci U S A 2018; 115:E3969-E3977. [PMID: 29632211 DOI: 10.1073/pnas.1719398115] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The nuclear pore complex (NPC) is an eightfold symmetrical channel providing selective transport of biomolecules across the nuclear envelope. Each NPC consists of ∼30 different nuclear pore proteins (Nups) all present in multiple copies per NPC. Significant progress has recently been made in the characterization of the vertebrate NPC structure. However, because of the estimated size differences between the vertebrate and yeast NPC, it has been unclear whether the NPC architecture is conserved between species. Here, we have developed a quantitative image analysis pipeline, termed nuclear rim intensity measurement (NuRIM), to precisely determine copy numbers for almost all Nups within native NPCs of budding yeast cells. Our analysis demonstrates that the majority of yeast Nups are present at most in 16 copies per NPC. This reveals a dramatic difference to the stoichiometry determined for the human NPC, suggesting that despite a high degree of individual Nup conservation, the yeast and human NPC architecture is significantly different. Furthermore, using NuRIM, we examined the effects of mutations on NPC stoichiometry. We demonstrate for two paralog pairs of key scaffold Nups, Nup170/Nup157 and Nup192/Nup188, that their altered expression leads to significant changes in the NPC stoichiometry inducing either voids in the NPC structure or substitution of one paralog by the other. Thus, our results not only provide accurate stoichiometry information for the intact yeast NPC but also reveal an intriguing compositional plasticity of the NPC architecture, which may explain how differences in NPC composition could arise in the course of evolution.
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30
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Imaging, Tracking and Computational Analyses of Virus Entry and Egress with the Cytoskeleton. Viruses 2018; 10:v10040166. [PMID: 29614729 PMCID: PMC5923460 DOI: 10.3390/v10040166] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 12/27/2022] Open
Abstract
Viruses have a dual nature: particles are “passive substances” lacking chemical energy transformation, whereas infected cells are “active substances” turning-over energy. How passive viral substances convert to active substances, comprising viral replication and assembly compartments has been of intense interest to virologists, cell and molecular biologists and immunologists. Infection starts with virus entry into a susceptible cell and delivers the viral genome to the replication site. This is a multi-step process, and involves the cytoskeleton and associated motor proteins. Likewise, the egress of progeny virus particles from the replication site to the extracellular space is enhanced by the cytoskeleton and associated motor proteins. This overcomes the limitation of thermal diffusion, and transports virions and virion components, often in association with cellular organelles. This review explores how the analysis of viral trajectories informs about mechanisms of infection. We discuss the methodology enabling researchers to visualize single virions in cells by fluorescence imaging and tracking. Virus visualization and tracking are increasingly enhanced by computational analyses of virus trajectories as well as in silico modeling. Combined approaches reveal previously unrecognized features of virus-infected cells. Using select examples of complementary methodology, we highlight the role of actin filaments and microtubules, and their associated motors in virus infections. In-depth studies of single virion dynamics at high temporal and spatial resolutions thereby provide deep insight into virus infection processes, and are a basis for uncovering underlying mechanisms of how cells function.
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31
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Nanopillar force measurements reveal actin-cap-mediated YAP mechanotransduction. Nat Cell Biol 2018; 20:262-271. [PMID: 29403039 DOI: 10.1038/s41556-017-0030-y] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 12/18/2017] [Indexed: 11/08/2022]
Abstract
A robust nanopillar platform with increased spatial resolution reveals that perinuclear forces, originating from stress fibres spanning the nucleus of fibroblasts, are significantly higher on these nanostructured substrates than the forces acting on peripheral adhesions. Many perinuclear adhesions embrace several nanopillars at once, pulling them into β1-integrin- and zyxin-rich clusters, which are able to translocate in the direction of cell motion without losing their tensile strength. The high perinuclear forces are greatly reduced upon inhibition of cell contractility or actin polymerization and disruption of the actin cap by KASH dominant-negative mutant expression. LMNA null fibroblasts have higher peripheral versus perinuclear forces, impaired perinuclear β1-integrin recruitment, as well as YAP nuclear translocation, functional alterations that can be rescued by lamin A expression. These highly tensed actin-cap fibres are required for YAP nuclear signalling and thus play far more important roles in sensing nanotopographies and mechanochemical signal conversion than previously thought.
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Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface. Viruses 2018; 10:v10010028. [PMID: 29316722 PMCID: PMC5795441 DOI: 10.3390/v10010028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 02/06/2023] Open
Abstract
Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles.
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