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Mii Y. Understanding and manipulating extracellular behaviors of Wnt ligands. In Vitro Cell Dev Biol Anim 2024; 60:441-448. [PMID: 38379096 DOI: 10.1007/s11626-024-00856-9] [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: 11/13/2023] [Accepted: 01/17/2024] [Indexed: 02/22/2024]
Abstract
Wnt, a family of secreted signaling proteins, serves diverse functions in embryogenesis, organogenesis, cancer, and stem cell functions. In the context of development, Wnt has been considered a representative morphogen, forming concentration gradients to give positional information to cells or tissues. However, although gradients are often illustrated in schemata, the reality of concentration gradients, or in other words, actual spatial distribution of Wnt ligands, and their behaviors in the extracellular space still remain poorly known. To understand extracellular behavior of Wnt ligands, quantitative analyses such as fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP) are highly informative because Wnt dispersal involves physical and biochemical processes, such as diffusion and binding to or dissociation from cell surface molecules, including heparan sulfate proteoglycans (HSPGs). Here, I briefly discuss representative methods to quantify morphogen dynamics. In addition, I discuss molecular manipulations of morphogens, mainly focusing on use of protein binders, and synthetic biology of morphogens as indicators of current and future directions in this field.
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Affiliation(s)
- Yusuke Mii
- National Institute for Basic Biology (NIBB) and Exploratory Research Center On Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, 444-8787, Japan.
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2
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Cambré A, Aertsen A. Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria. Microbiol Mol Biol Rev 2020; 84:e00008-20. [PMID: 33115939 PMCID: PMC7599038 DOI: 10.1128/mmbr.00008-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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3
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Iino R, Iida T, Nakamura A, Saita EI, You H, Sako Y. Single-molecule imaging and manipulation of biomolecular machines and systems. Biochim Biophys Acta Gen Subj 2017; 1862:241-252. [PMID: 28789884 DOI: 10.1016/j.bbagen.2017.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/23/2017] [Accepted: 08/03/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. SCOPE OF REVIEW We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. MAJOR CONCLUSIONS Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Ryota Iino
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan.
| | - Tatsuya Iida
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Akihiko Nakamura
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Ei-Ichiro Saita
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, Japan
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, China.
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Cortical Polarity of the RING Protein PAR-2 Is Maintained by Exchange Rate Kinetics at the Cortical-Cytoplasmic Boundary. Cell Rep 2016; 16:2156-2168. [DOI: 10.1016/j.celrep.2016.07.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 01/10/2016] [Accepted: 07/20/2016] [Indexed: 11/20/2022] Open
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6
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Uchihashi T, Watanabe H, Fukuda S, Shibata M, Ando T. Functional extension of high-speed AFM for wider biological applications. Ultramicroscopy 2016; 160:182-196. [DOI: 10.1016/j.ultramic.2015.10.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 09/25/2015] [Accepted: 10/12/2015] [Indexed: 11/24/2022]
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7
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Zhou Y, Mao H, Joddar B, Umeki N, Sako Y, Wada KI, Nishioka C, Takahashi E, Wang Y, Ito Y. The significance of membrane fluidity of feeder cell-derived substrates for maintenance of iPS cell stemness. Sci Rep 2015; 5:11386. [PMID: 26065582 PMCID: PMC4464345 DOI: 10.1038/srep11386] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/22/2015] [Indexed: 11/09/2022] Open
Abstract
The biological activity of cell-derived substrates to maintain undifferentiated murine-induced pluripotent stem (iPS) cells was correlated to membrane fluidity as a new parameter of cell culture substrates. Murine embryonic fibroblasts (MEFs) were employed as feeder cells and their membrane fluidity was tuned by chemical fixation using formaldehyde (FA). Membrane fluidity was evaluated by real-time single-molecule observations of green fluorescent protein-labeled epidermal growth factor receptors on chemically fixed MEFs. Biological activity was monitored by colony formation of iPS cells. Treatment with a low concentration of FA sustained the membrane fluidity and biological activity, which were comparable to those of mitomycin C-treated MEFs. The biological activity was further confirmed by sustained expression of alkaline phosphatase, SSEA-1, and other pluripotency markers in iPS cells after 3-5 days of culture on FA-fixed MEFs. Chemical fixation of feeder cells has several advantages such as providing ready-to-use culture substrates without contamination by proliferating feeder cells. Therefore, our results provide an important basis for the development of chemically fixed culture substrates for pluripotent stem cell culture as an alternative to conventional treatment by mitomycin C or x-ray irradiation.
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Affiliation(s)
- Yue Zhou
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- School of Nursing, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing, Jiangsu Province 210023, China
- Department of Regenerative Medicine, School of Pharmaceutical Science, Jilin University, No.1266 Fujin Road, Changchun 130021, China
| | - Hongli Mao
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Binata Joddar
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Nobuhisa Umeki
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ken-Ichi Wada
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Chieko Nishioka
- Support Unit for Animal Experiment, Research Resources Center, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Eiki Takahashi
- Support Unit for Animal Experiment, Research Resources Center, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yi Wang
- Department of Regenerative Medicine, School of Pharmaceutical Science, Jilin University, No.1266 Fujin Road, Changchun 130021, China
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1Hirosawa, Wako, Saitama 351-0198, Japan
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Kepten E, Weron A, Sikora G, Burnecki K, Garini Y. Guidelines for the fitting of anomalous diffusion mean square displacement graphs from single particle tracking experiments. PLoS One 2015; 10:e0117722. [PMID: 25680069 PMCID: PMC4334513 DOI: 10.1371/journal.pone.0117722] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 12/30/2014] [Indexed: 12/15/2022] Open
Abstract
Single particle tracking is an essential tool in the study of complex systems and biophysics and it is commonly analyzed by the time-averaged mean square displacement (MSD) of the diffusive trajectories. However, past work has shown that MSDs are susceptible to significant errors and biases, preventing the comparison and assessment of experimental studies. Here, we attempt to extract practical guidelines for the estimation of anomalous time averaged MSDs through the simulation of multiple scenarios with fractional Brownian motion as a representative of a large class of fractional ergodic processes. We extract the precision and accuracy of the fitted MSD for various anomalous exponents and measurement errors with respect to measurement length and maximum time lags. Based on the calculated precision maps, we present guidelines to improve accuracy in single particle studies. Importantly, we find that in some experimental conditions, the time averaged MSD should not be used as an estimator.
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Affiliation(s)
- Eldad Kepten
- Physics Department & Institute of Nanotechnology, Bar Ilan University, Ramat Gan, Israel
| | - Aleksander Weron
- Hugo Steinhaus Center, Institute of Mathematics and Computer Science, Wroclaw University of Technology, Wroclaw, Poland
| | - Grzegorz Sikora
- Hugo Steinhaus Center, Institute of Mathematics and Computer Science, Wroclaw University of Technology, Wroclaw, Poland
| | - Krzysztof Burnecki
- Hugo Steinhaus Center, Institute of Mathematics and Computer Science, Wroclaw University of Technology, Wroclaw, Poland
| | - Yuval Garini
- Physics Department & Institute of Nanotechnology, Bar Ilan University, Ramat Gan, Israel
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9
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Yao Z, Carballido-López R. Fluorescence Imaging for Bacterial Cell Biology: From Localization to Dynamics, From Ensembles to Single Molecules. Annu Rev Microbiol 2014; 68:459-76. [DOI: 10.1146/annurev-micro-091213-113034] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhizhong Yao
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France;
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10
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Li R, Fowler JA, Todd BA. Calculated rates of diffusion-limited reactions in a three-dimensional network of connected compartments: application to porous catalysts and biological systems. PHYSICAL REVIEW LETTERS 2014; 113:028303. [PMID: 25062243 DOI: 10.1103/physrevlett.113.028303] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Indexed: 06/03/2023]
Abstract
We describe the diffusion limit for reaction rates in a three-dimensional system of connected compartments. This model exhibits the length-scale dependent diffusion that can be observed in many heterogeneous environments, such as porous catalysts and biological environments. We obtain a simple analytical expression for the diffusion limit applicable to any scale of the compartment confinement. This diffusion limit exceeds the classic Smoluchowski diffusion limit that was derived for homogeneous environments but is often applied to biological reactions in heterogeneous environments. We expect our new diffusion limit to provide a more appropriate upper bound on reaction rates in biological systems, porous structures, and other heterogeneous environments where obstacles create local confinement.
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Affiliation(s)
- Ran Li
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907, USA and Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Justin A Fowler
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Brian A Todd
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
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11
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Uphoff S, Kapanidis AN. Studying the organization of DNA repair by single-cell and single-molecule imaging. DNA Repair (Amst) 2014; 20:32-40. [PMID: 24629485 PMCID: PMC4119245 DOI: 10.1016/j.dnarep.2014.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 12/26/2022]
Abstract
Single-cell experiments to study stochastic events and heterogeneity in DNA repair. Quantifying DNA repair protein concentration, diffusion, and localization in cells. Direct observation of DNA repair using photoactivated single-molecule tracking.
DNA repair safeguards the genome against a diversity of DNA damaging agents. Although the mechanisms of many repair proteins have been examined separately in vitro, far less is known about the coordinated function of the whole repair machinery in vivo. Furthermore, single-cell studies indicate that DNA damage responses generate substantial variation in repair activities across cells. This review focuses on fluorescence imaging methods that offer a quantitative description of DNA repair in single cells by measuring protein concentrations, diffusion characteristics, localizations, interactions, and enzymatic rates. Emerging single-molecule and super-resolution microscopy methods now permit direct visualization of individual proteins and DNA repair events in vivo. We expect much can be learned about the organization of DNA repair by linking cell heterogeneity to mechanistic observations at the molecular level.
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Affiliation(s)
- Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
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12
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Ploetz E, Visser B, Slingenbergh W, Evers K, Martinez-Martinez D, Pei YT, Feringa BL, De Hosson JTM, Cordes T, van Dorp WF. Selective functionalization of patterned glass surfaces. J Mater Chem B 2014; 2:2606-2615. [DOI: 10.1039/c3tb21763a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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High-speed atomic force microscopy combined with inverted optical microscopy for studying cellular events. Sci Rep 2013; 3:2131. [PMID: 23823461 PMCID: PMC3701170 DOI: 10.1038/srep02131] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/10/2013] [Indexed: 11/08/2022] Open
Abstract
A hybrid atomic force microscopy (AFM)-optical fluorescence microscopy is a powerful tool for investigating cellular morphologies and events. However, the slow data acquisition rates of the conventional AFM unit of the hybrid system limit the visualization of structural changes during cellular events. Therefore, high-speed AFM units equipped with an optical/fluorescence detection device have been a long-standing wish. Here we describe the implementation of high-speed AFM coupled with an optical fluorescence microscope. This was accomplished by developing a tip-scanning system, instead of a sample-scanning system, which operates on an inverted optical microscope. This novel device enabled the acquisition of high-speed AFM images of morphological changes in individual cells. Using this instrument, we conducted structural studies of living HeLa and 3T3 fibroblast cell surfaces. The improved time resolution allowed us to image dynamic cellular events.
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14
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Liu X, Tang M, Zhang T, Hu Y, Zhang S, Kong L, Xue Y. Determination of a threshold dose to reduce or eliminate CdTe-induced toxicity in L929 cells by controlling the exposure dose. PLoS One 2013; 8:e59359. [PMID: 23577063 PMCID: PMC3618428 DOI: 10.1371/journal.pone.0059359] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 02/13/2013] [Indexed: 12/17/2022] Open
Abstract
With the widespread use of quantum dots (QDs), the likelihood of exposure to quantum dots has increased substantially. The application of quantum dots in numerous biomedical areas requires detailed studies on their toxicity. In this study, we aimed to determine the threshold dose which reduced or eliminated CdTe-induced toxicity in L929 cells by controlling the exposure dose. We established a cellular model of acute exposure to CdTe QDs. Cells were exposed to different concentrations of CdTe QDs (2.2 nm and 3.5 nm) followed by illustrative cytotoxicity analysis. The results showed that low concentrations of CdTe QDs (under 10 µg/mL) promoted cell viability, caused no obvious effect on the rate of cell apoptosis, intracellular calcium levels and changes in mitochondrial membrane potential, while high concentrations significantly inhibited cell viability. In addition, reactive oxygen species in the 10 µg/mL-treated group was significantly reduced compared with the control group. In summary, the cytotoxicity of CdTe QDs on L929 cell is dose-dependent, time-dependent and size-dependent. Low concentrations of CdTe QDs (below 10 µg/mL) may be nontoxic and safe in L929 cells, whereas high concentrations (above 10 µg/mL) may be toxic resulting in inhibition of proliferation and induction of apoptosis in L929 cells.
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Affiliation(s)
- Xiaorun Liu
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, China
| | - Meng Tang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, China
- * E-mail:
| | - Ting Zhang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, China
| | - Yuanyuan Hu
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, China
| | - Shanshan Zhang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, China
| | - Lu Kong
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, China
| | - Yuying Xue
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, China
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15
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Affiliation(s)
- Tie Xia
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructures and Nanotechnology, Chinese Academy of Sciences, Beijing 100190, China;
| | - Nan Li
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructures and Nanotechnology, Chinese Academy of Sciences, Beijing 100190, China;
| | - Xiaohong Fang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructures and Nanotechnology, Chinese Academy of Sciences, Beijing 100190, China;
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16
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New insights into replisome fluidity during chromosome replication. Trends Biochem Sci 2012; 38:195-203. [PMID: 23153958 DOI: 10.1016/j.tibs.2012.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/09/2012] [Accepted: 10/12/2012] [Indexed: 11/21/2022]
Abstract
Several paradigm shifting advances have recently been made on the composition and function of the chromosomal DNA replication machinery. Replisomes appear to be more fluid and dynamic than ever imagined, enabling rapid and efficient bypass of roadblocks and template lesions while faithfully replicating chromosomal DNA. This fluidity is determined by many layers of regulation, which reach beyond the role of replisome components themselves. In fact, recent studies show that additional polymerases, post-transcriptional modifications, and chromatin structure are required for complete chromosome duplication. Many of these factors are involved with the more complex events that take place during lagging-strand synthesis. These, and other recent discoveries, are the focus of this review.
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17
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Yang J, Pearson JE. Origins of concentration dependence of waiting times for single-molecule fluorescence binding. J Chem Phys 2012; 136:244506. [PMID: 22755586 DOI: 10.1063/1.4729947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Binary fluorescence time series obtained from single-molecule imaging experiments can be used to infer protein binding kinetics, in particular, association and dissociation rate constants from waiting time statistics of fluorescence intensity changes. In many cases, rate constants inferred from fluorescence time series exhibit nonintuitive dependence on ligand concentration. Here, we examine several possible mechanistic and technical origins that may induce ligand dependence of rate constants. Using aggregated Markov models, we show under the condition of detailed balance that non-fluorescent bindings and missed events due to transient interactions, instead of conformation fluctuations, may underly the dependence of waiting times and thus apparent rate constants on ligand concentrations. In general, waiting times are rational functions of ligand concentration. The shape of concentration dependence is qualitatively affected by the number of binding sites in the single molecule and is quantitatively tuned by model parameters. We also show that ligand dependence can be caused by non-equilibrium conditions which result in violations of detailed balance and require an energy source. As to a different but significant mechanism, we examine the effect of ambient buffers that can substantially reduce the effective concentration of ligands that interact with the single molecules. To demonstrate the effects by these mechanisms, we applied our results to analyze the concentration dependence in a single-molecule experiment EGFR binding to fluorophore-labeled adaptor protein Grb2 by Morimatsu et al. [Proc. Natl. Acad. Sci. U.S.A. 104, 18013 (2007)].
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Affiliation(s)
- Jin Yang
- Chinese Academy of Sciences and Max Plank Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China.
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18
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Webb SED, Zanetti-Domingues L, Coles BC, Rolfe DJ, Wareham RJ, Martin-Fernandez ML. Multicolour single molecule imaging on cells using a supercontinuum source. BIOMEDICAL OPTICS EXPRESS 2012; 3:400-406. [PMID: 22435089 PMCID: PMC3296529 DOI: 10.1364/boe.3.000400] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 01/20/2012] [Accepted: 01/30/2012] [Indexed: 05/31/2023]
Abstract
Multicolour single molecule fluorescence imaging enables the study of multiple proteins in the membranes of living cells. We describe the use of a supercontinuum laser as the excitation source, show its comparability with multiplexed single-wavelength lasers and demonstrate that it can be used to study membrane proteins such as the ErbB receptor family. We discuss the benefits of white-light sources for single molecule fluorescence, in particular their ease of use and the freedom to use the most appropriate dye without being constrained by available laser wavelengths.
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Affiliation(s)
- Stephen E. D. Webb
- Central Laser Facility, Science & Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK
| | - Laura Zanetti-Domingues
- Central Laser Facility, Science & Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK
| | - Benjamin C. Coles
- Central Laser Facility, Science & Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK
| | - Daniel J. Rolfe
- Central Laser Facility, Science & Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK
| | - Richard J. Wareham
- Department of Engineering, University of Cambridge, Trumpington St, Cambridge CB2 1PZ, UK
| | - Marisa L. Martin-Fernandez
- Central Laser Facility, Science & Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK
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Lee SS, Horvath P, Pelet S, Hegemann B, Lee LP, Peter M. Quantitative and dynamic assay of single cell chemotaxis. Integr Biol (Camb) 2012; 4:381-90. [PMID: 22230969 DOI: 10.1039/c2ib00144f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We have developed a single-cell assay platform that allows quantitative analysis of single cell chemotaxis by dynamic morphogenetic gradients, subcellular microscopic imaging and automated image analysis, and have applied these to measure cellular polarization of budding yeast. The computer-controlled microfluidic device regulates the gradient profile at any given time, and allows quantitative monitoring of cell morphology and the localization and expression of specific marker proteins during the dynamic polarization process. With this integrated experimental system, we compare the polarized signaling response of wild-type and far1-H7 mutant cells, which express a truncated Far1 protein unable to interact with Cdc24. Our results confirm that Far1 functions as an adaptor that recruits polarity establishment proteins to the site of extracellular signaling. Moreover, by changing the gradient profile and estimating the number of bound surface receptors, we quantitatively address why surprisingly small differences in pheromone concentration across yeast cells can be amplified into a robust polarity axis. This integrated single cell experimental platform thus opens the possibility to quantitatively investigate the molecular regulatory mechanism of chemotaxis in yeast, which serves as a paradigm to understand the fundamental processes involved in cancer metastasis, angiogenesis and axon generation.
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Affiliation(s)
- Sung Sik Lee
- Institute of Biochemistry, ETH Zurich, Zurich, CH 8093, Switzerland
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Functioning nanomachines seen in real-time in living bacteria using single-molecule and super-resolution fluorescence imaging. Int J Mol Sci 2011; 12:2518-42. [PMID: 21731456 PMCID: PMC3127132 DOI: 10.3390/ijms12042518] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/07/2011] [Accepted: 04/11/2011] [Indexed: 11/19/2022] Open
Abstract
Molecular machines are examples of “pre-established” nanotechnology, driving the basic biochemistry of living cells. They encompass an enormous range of function, including fuel generation for chemical processes, transport of molecular components within the cell, cellular mobility, signal transduction and the replication of the genetic code, amongst many others. Much of our understanding of such nanometer length scale machines has come from in vitro studies performed in isolated, artificial conditions. Researchers are now tackling the challenges of studying nanomachines in their native environments. In this review, we outline recent in vivo investigations on nanomachines in model bacterial systems using state-of-the-art genetics technology combined with cutting-edge single-molecule and super-resolution fluorescence microscopy. We conclude that single-molecule and super-resolution fluorescence imaging provide powerful tools for the biochemical, structural and functional characterization of biological nanomachines. The integrative spatial, temporal, and single-molecule data obtained simultaneously from fluorescence imaging open an avenue for systems-level single-molecule cellular biophysics and in vivo biochemistry.
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22
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Suzuki Y, Yokokawa M, Yoshimura SH, Takeyasu K. Biological Application of Fast-Scanning Atomic Force Microscopy. SCANNING PROBE MICROSCOPY IN NANOSCIENCE AND NANOTECHNOLOGY 2 2011. [DOI: 10.1007/978-3-642-10497-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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23
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Lidstrom ME, Konopka MC. The role of physiological heterogeneity in microbial population behavior. Nat Chem Biol 2010; 6:705-12. [PMID: 20852608 DOI: 10.1038/nchembio.436] [Citation(s) in RCA: 207] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
As the ability to analyze individual cells in microbial populations expands, it is becoming apparent that isogenic microbial populations contain substantial cell-to-cell differences in physiological parameters such as growth rate, resistance to stress and regulatory circuit output. Subpopulations exist that are manyfold different in these parameters from the population average, and these differences arise by stochastic processes. Such differences can dramatically affect the response of cells to perturbations, especially stress, which in turn dictates overall population response. Defining the role of cell-to-cell heterogeneity in population behavior is important for understanding population-based research problems, including those involving infecting populations, normal flora and bacterial populations in water and soils. Emerging technological breakthroughs are poised to transform single-cell analysis and are critical for the next phase of insights into physiological heterogeneity in the near future. These include technologies for multiparameter analysis of live cells, with downstream processing and analysis.
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Affiliation(s)
- Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA.
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24
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Ta H, Kiel A, Wahl M, Herten DP. Experimental approach to extend the range for counting fluorescent molecules based on photon-antibunching. Phys Chem Chem Phys 2010; 12:10295-300. [PMID: 20603676 DOI: 10.1039/c0cp00363h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In single-molecule fluorescence spectroscopy photon-antibunching is frequently used to prove the occurrence of single fluorophores. Furthermore, the relative frequency of coincident photon pairs was also used to determine the number of fluorophores in the diffraction limited observation volume of a confocal microscope. However, the ability to count fluorophores is so far limited to approximately 3 molecules due to saturation of the calibration curve with increasing number of fluorophores. Recently, we introduced a novel theoretical framework for counting the number of emitting molecules by analyzing photon-distributions acquired with a confocal microscope using four single-photon detectors. Here, we present the experimental realization of the proposed scheme in a confocal setup using novel multi-channel photon-counting electronics and DNA constructs that were labelled with five fluorophores. Our experimental results give a clear correlation between the number of estimated fluorophores and the number of bleaching steps for DNA probes conjugated with five ATTO647N labels with an error of approximately 20%. Moreover, we could acquire experimental data for up to 15 fluorophores indicating the simultaneous occurrence of three DNA probes. Our experiments put into perspective that the analysis of photon-distributions acquired with four detection channels is suited to count the number of fluorescently labelled molecules in larger aggregates or clusters with potential for applications in molecular and cell biology and for time-resolved analysis of multi-chromophoric compounds in material sciences.
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Affiliation(s)
- Haisen Ta
- Cellnetworks Cluster and Institute for Physical Chemistry, Heidelberg Univ., Im Neuenheimer Feld 267, D-69214 Heidelberg, Germany
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25
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Hibino K, Shibata T, Yanagida T, Sako Y. A RasGTP-induced conformational change in C-RAF is essential for accurate molecular recognition. Biophys J 2009; 97:1277-87. [PMID: 19720015 DOI: 10.1016/j.bpj.2009.05.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 05/22/2009] [Accepted: 05/28/2009] [Indexed: 10/20/2022] Open
Abstract
The dysregulation of Ras-RAF signaling is associated with many types of human cancer. However, the kinetic and dynamic features of the mutual molecular recognition of Ras and RAF remain unknown. Here, we developed a technique for imaging single-pair fluorescence resonance energy transfer in living cells, and coupled this technique to single-molecule kinetic analysis to investigate how C-RAF (a subtype of RAF) molecules distinguish the active form of Ras (RasGTP) from the inactive form (RasGDP). Functional fragments of C-RAF containing the Ras-binding domains did not detect the switch in Ras activity in living cells as efficiently as did C-RAF. Single-molecule analysis showed that RasGDP associates with closed-conformation C-RAF, whereas the association of C-RAF with RasGTP immediately triggers the open RAF conformation, which induces an effective interaction between C-RAF and RasGTP. Spontaneous conformational changes from closed C-RAF to the open form rarely occur in quiescent cells. The conformational change in C-RAF is so important to Ras-RAF molecular recognition that C-RAF mutants lacking the conformational change cannot distinguish between RasGDP and RasGTP. The manipulation of the conformation of an effector molecule is a newly identified function of RasGTP.
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Affiliation(s)
- Kayo Hibino
- Cellular Informatics Laboratory, RIKEN, Wako, Japan
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26
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Mehta K, Hoppe AD, Kainkaryam R, Woolf PJ, Linderman JJ. A computational approach to inferring cellular protein-binding affinities from quantitative fluorescence resonance energy transfer imaging. Proteomics 2009; 9:5371-83. [PMID: 19834887 DOI: 10.1002/pmic.200800494] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 09/01/2009] [Indexed: 12/22/2022]
Abstract
Fluorescence resonance energy transfer (FRET) microscopy can measure the spatial distribution of protein interactions inside live cells. Such experiments give rise to complex data sets with many images of single cells, motivating data reduction and abstraction. In particular, determination of the value of the equilibrium dissociation constant (K(d)) will provide a quantitative measure of protein-protein interactions, which is essential to reconstructing cellular signaling networks. Here, we investigate the feasibility of using quantitative FRET imaging of live cells to estimate the local value of K(d) for two interacting labeled molecules. An algorithm is developed to infer the values of K(d) using the intensity of individual voxels of 3-D FRET microscopy images. The performance of our algorithm is investigated using synthetic test data, both in the absence and in the presence of endogenous (unlabeled) proteins. The influence of optical blurring caused by the microscope (confocal or wide field) and detection noise on the accuracy of K(d) inference is studied. We show that deconvolution of images followed by analysis of intensity data at local level can improve the estimate of K(d). Finally, the performance of this algorithm using cellular data on the interaction between yellow fluorescent protein-Rac and cyan fluorescent protein-PBD in mammalian cells is shown.
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Affiliation(s)
- Khamir Mehta
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2136, USA
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27
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Needleman DJ, Groen A, Ohi R, Maresca T, Mirny L, Mitchison T. Fast microtubule dynamics in meiotic spindles measured by single molecule imaging: evidence that the spindle environment does not stabilize microtubules. Mol Biol Cell 2009; 21:323-33. [PMID: 19940016 PMCID: PMC2808228 DOI: 10.1091/mbc.e09-09-0816] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Metaphase spindles are steady-state ensembles of microtubules. We used single molecule imaging to measure tubulin dynamics in spindles and non-spindle assemblies in Xenopus egg extract. Our results argue that the high density of microtubules in spindles is caused by local enhancement of nucleation, and not by local stabilization. Metaphase spindles are steady-state ensembles of microtubules that turn over rapidly and slide poleward in some systems. Since the discovery of dynamic instability in the mid-1980s, models for spindle morphogenesis have proposed that microtubules are stabilized by the spindle environment. We used single molecule imaging to measure tubulin turnover in spindles, and nonspindle assemblies, in Xenopus laevis egg extracts. We observed many events where tubulin molecules spend only a few seconds in polymer and thus are difficult to reconcile with standard models of polymerization dynamics. Our data can be quantitatively explained by a simple, phenomenological model—with only one adjustable parameter—in which the growing and shrinking of microtubule ends is approximated as a biased random walk. Microtubule turnover kinetics did not vary with position in the spindle and were the same in spindles and nonspindle ensembles nucleated by Tetrahymena pellicles. These results argue that the high density of microtubules in spindles compared with bulk cytoplasm is caused by local enhancement of nucleation and not by local stabilization. It follows that the key to understanding spindle morphogenesis will be to elucidate how nucleation is spatially controlled.
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Affiliation(s)
- Daniel J Needleman
- School of Engineering and Applied Sciences, Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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28
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Hibino K, Hiroshima M, Takahashi M, Sako Y. Single-molecule imaging of fluorescent proteins expressed in living cells. Methods Mol Biol 2009; 544:451-60. [PMID: 19488718 DOI: 10.1007/978-1-59745-483-4_30] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This chapter focuses on single-molecule imaging (SMI) in living cells using green fluorescent protein (GFP) or its related fluorescent protein tags (GFPs). Use of GFPs is a convenient technique to achieve molecular imaging of most proteins in living cells. However, because of difficulties in preparing samples suitable for SMI and the instability of fluorescence signals, special care is required for SMI using GFPs in living cells. Techniques for vector preparation, protein expression, sample preparation, microscopy, and image processing for SMI of GFPs in living cells are discussed in this chapter, along with examples of imaging applications. Double labeling of single molecules and single-pair fluorescent resonance energy transfer (spFRET) are possible in living cells using GFP and YFP as fluorescent tags. The limitations of SMI using GFPs are also discussed.
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Affiliation(s)
- Kayo Hibino
- Cellular Informatics Laboratory, 2-1 Hirosawa, 351-0198, RIKEN, Wako, Japan
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29
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Espenel C, Margeat E, Dosset P, Arduise C, Le Grimellec C, Royer CA, Boucheix C, Rubinstein E, Milhiet PE. Single-molecule analysis of CD9 dynamics and partitioning reveals multiple modes of interaction in the tetraspanin web. ACTA ACUST UNITED AC 2008; 182:765-76. [PMID: 18710926 PMCID: PMC2518714 DOI: 10.1083/jcb.200803010] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Tetraspanins regulate cell migration, sperm–egg fusion, and viral infection. Through interactions with one another and other cell surface proteins, tetraspanins form a network of molecular interactions called the tetraspanin web. In this study, we use single-molecule fluorescence microscopy to dissect dynamics and partitioning of the tetraspanin CD9. We show that lateral mobility of CD9 in the plasma membrane is regulated by at least two modes of interaction that each exhibit specific dynamics. The majority of CD9 molecules display Brownian behavior but can be transiently confined to an interaction platform that is in permanent exchange with the rest of the membrane. These platforms, which are enriched in CD9 and its binding partners, are constant in shape and localization. Two CD9 molecules undergoing Brownian trajectories can also codiffuse, revealing extra platform interactions. CD9 mobility and partitioning are both dependent on its palmitoylation and plasma membrane cholesterol. Our data show the high dynamic of interactions in the tetraspanin web and further indicate that the tetraspanin web is distinct from raft microdomains.
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Affiliation(s)
- Cedric Espenel
- Institut National de la Santé et de la Recherche Medicale, Unité 554, Montpellier, France
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30
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Vassanelli S, Bandiera L, Borgo M, Cellere G, Santoni L, Bersani C, Salamon M, Zaccolo M, Lorenzelli L, Girardi S, Maschietto M, Dal Maschio M, Paccagnella A. Space and time-resolved gene expression experiments on cultured mammalian cells by a single-cell electroporation microarray. N Biotechnol 2008; 25:55-67. [PMID: 18504020 DOI: 10.1016/j.nbt.2008.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2007] [Revised: 02/07/2008] [Accepted: 03/03/2008] [Indexed: 02/04/2023]
Abstract
Single-cell experiments represent the next frontier for biochemical and gene expression research. Although bulk-scale methods averaging populations of cells have been traditionally used to investigate cellular behavior, they mask individual cell features and can lead to misleading or insufficient biological results. We report on a single-cell electroporation microarray enabling the transfection of pre-selected individual cells at different sites within the same culture (space-resolved), at arbitrarily chosen time points and even sequentially to the same cells (time-resolved). Delivery of impermeant molecules by single-cell electroporation was first proven to be finely tunable by acting on the electroporation protocol and then optimized for transfection of nucleic acids into Chinese Hamster Ovary (CHO-K1) cells. We focused on DNA oligonucleotides (ODNs), short interfering RNAs (siRNAs), and DNA plasmid vectors, thus providing a versatile and easy-to-use platform for time-resolved gene expression experiments in single mammalian cells.
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Affiliation(s)
- S Vassanelli
- University of Padova, Department of Human Anatomy and Physiology, Section of Physiology, via Marzolo 3 - 35131, Padova, Italy.
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31
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Kvach MV, Ustinov AV, Stepanova IA, Malakhov AD, Skorobogatyi MV, Shmanai VV, Korshun VA. A Convenient Synthesis of Cyanine Dyes: Reagents for the Labeling of Biomolecules. European J Org Chem 2008. [DOI: 10.1002/ejoc.200701190] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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32
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Hall D. Analysis and interpretation of two-dimensional single-particle tracking microscopy measurements: effect of local surface roughness. Anal Biochem 2008; 377:24-32. [PMID: 18358822 DOI: 10.1016/j.ab.2008.02.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 12/29/2007] [Accepted: 02/19/2008] [Indexed: 10/22/2022]
Abstract
Methodological advances in light microscopy have made it possible to record the motions of individual lipid and protein molecules resident in the membrane of living cells down to the nanometer level of precision in the x, y plane. Such measurement of a single molecule's trajectory for a sufficiently long period of time or the measurement of multiple molecules' trajectories for a shorter period of time can in principle provide the necessary information to derive the particle's macroscopic two-dimensional-diffusion coefficient-a quantity of vital biological interest. However, one drawback of the light microscopy procedures used in such experiments is their relatively poor discriminatory capability for determining spatial differences along the z axis in comparison to those in the x, y plane. In this study we used computer simulation to examine the likely effect of local surface roughness over the nanometer to micrometer scale on the determination of diffusion constants in the membrane bilayer by the use of such optical-microscope-based single-particle tracking (SPT) procedures. We specifically examined motion of a single molecule along (i) a locally planar and (ii) a locally rough surface. Our results indicate a need for caution in applying overly simplistic analytical strategies to the analysis of data from SPT measurements and provide upper and lower bounds for the likely degree of error introduced on the basis of surface roughness effects alone. Additionally we present an empirical method based on an autocorrelation function approach that may prove useful in identifying the existence of surface roughness and give some idea of its extent.
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Affiliation(s)
- Damien Hall
- Institute for Protein Research, Osaka University. 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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33
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Nagaya H, Tamura T, Higa-Nishiyama A, Ohashi K, Takeuchi M, Hashimoto H, Hatsuzawa K, Kinjo M, Okada T, Wada I. Regulated motion of glycoproteins revealed by direct visualization of a single cargo in the endoplasmic reticulum. ACTA ACUST UNITED AC 2008; 180:129-43. [PMID: 18195104 PMCID: PMC2213621 DOI: 10.1083/jcb.200704078] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The quality of cargo proteins in the endoplasmic reticulum (ER) is affected by their motion during folding. To understand how the diffusion of secretory cargo proteins is regulated in the ER, we directly analyze the motion of a single cargo molecule using fluorescence imaging/fluctuation analyses. We find that the addition of two N-glycans onto the cargo dramatically alters their diffusion by transient binding to membrane components that are confined by hyperosmolarity. Via simultaneous observation of a single cargo and ER exit sites (ERESs), we could exclude ERESs as the binding sites. Remarkably, actin cytoskeleton was required for the transient binding. These results provide a molecular basis for hypertonicity-induced immobilization of cargo, which is dependent on glycosylation at multiple sites but not the completion of proper folding. We propose that diffusion of secretory glycoproteins in the ER lumen is controlled from the cytoplasm to reduce the chances of aggregation.
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Affiliation(s)
- Hisao Nagaya
- Department of Cell Science, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
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Abstract
In the past decade, advances in molecular biology such as the development of non-invasive single molecule imaging techniques have given us a window into the intricate biochemical activities that occur inside cells. In this chapter we review four distinct theoretical and simulation frameworks: (i) non-spatial and deterministic, (ii) spatial and deterministic, (iii) non-spatial and stochastic and (iv) spatial and stochastic. Each framework can be suited to modelling and interpreting intracellular reaction kinetics. By estimating the fundamental length scales, one can roughly determine which models are best suited for the particular reaction pathway under study. We discuss differences in prediction between the four modelling methodologies. In particular we show that taking into account noise and space does not simply add quantitative predictive accuracy but may also lead to qualitatively different physiological predictions, unaccounted for by classical deterministic models.
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Affiliation(s)
- Ramon Grima
- Institute for Mathematical Sciences, Imperial College, London ()
| | - Santiago Schnell
- Indiana University School of Informatics and Biocomplexity Institute, 1900 E 10th St, Eigenmann Hall 906, Bloomington, IN 47406 ()
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35
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Affiliation(s)
- Rudi Balling
- Helmholtz Centre for Infection Research, Braunschweig, Germany.
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36
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Abstract
Optical imaging in live cells has provided a wealth of information regarding the various biological mechanisms, including using genetically coded green-fluorescent protein-conjugated organic dye molecules and, more recently, highly luminescent quantum dots as optical tags for the target biomolecules. Cells are inherently complex, grow constantly and have autofluorescence covering the entire visible spectrum ranging from green to red. At the single quantum-emitter level, it is often difficult to distinguish optical probes from fortuitous fluorophores inside living cells owing to complexity and constant evolvement. We have developed photoswitchable nanoparticles–optical nanoprobes that can be highlighted in either red or green during fluorescence imaging. Such optically addressable nanoprobes offer unambiguous detection of sites of biological interactions, and successfully implementing such optically switchable nanoprobes should greatly reduce the occurence of false-positives in biomedical imaging and unambiguous detections.
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Affiliation(s)
- Wuwei Wu
- Washington State University, Department of Chemistry, Pullman, WA 99164, USA
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37
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LeDuc P, Schwartz R. Computational models of molecular self-organization in cellular environments. Cell Biochem Biophys 2007; 48:16-31. [PMID: 17703065 DOI: 10.1007/s12013-007-0012-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 01/08/2023]
Abstract
The cellular environment creates numerous obstacles to efficient chemistry, as molecular components must navigate through a complex, densely crowded, heterogeneous, and constantly changing landscape in order to function at the appropriate times and places. Such obstacles are especially challenging to self-organizing or self-assembling molecular systems, which often need to build large structures in confined environments and typically have high-order kinetics that should make them exquisitely sensitive to concentration gradients, stochastic noise, and other non-ideal reaction conditions. Yet cells nonetheless manage to maintain a finely tuned network of countless molecular assemblies constantly forming and dissolving with a robustness and efficiency generally beyond what human engineers currently can achieve under even carefully controlled conditions. Significant advances in high-throughput biochemistry and genetics have made it possible to identify many of the components and interactions of this network, but its scale and complexity will likely make it impossible to understand at a global, systems level without predictive computational models. It is thus necessary to develop a clear understanding of how the reality of cellular biochemistry differs from the ideal models classically assumed by simulation approaches and how simulation methods can be adapted to accurately reflect biochemistry in the cell, particularly for the self-organizing systems that are most sensitive to these factors. In this review, we present approaches that have been undertaken from the modeling perspective to address various ways in which self-organization in the cell differs from idealized models.
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Affiliation(s)
- Philip LeDuc
- Department of Mechanical Engineering and Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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38
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Drbal K, Moertelmaier M, Holzhauser C, Muhammad A, Fuertbauer E, Howorka S, Hinterberger M, Stockinger H, Schütz GJ. Single-molecule microscopy reveals heterogeneous dynamics of lipid raft components upon TCR engagement. Int Immunol 2007; 19:675-84. [PMID: 17446208 DOI: 10.1093/intimm/dxm032] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The existence of lipid rafts and their importance for immunoreceptor signaling is highly debated. By non-invasive single molecule imaging, we analyzed the dynamics of the T-cell antigen receptor (TCR), the lipid raft-associated glycosylphosphatidylinositol (GPI) proteins CD48 and CD59 and the major leukocyte phosphatase CD45 in living naive T lymphocytes. TCR triggering induced the immobilization of CD45 and CD48 at different positions within the T-cell interface. The second GPI protein, CD59, did not co-immobilize indicating lipid raft heterogeneity in living T lymphocytes. A novel biochemical approach confirmed that lipid raft components are not associated in the plasma membrane of resting cells, and variably associate with specific receptors to distinct lipid rafts upon activation.
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Affiliation(s)
- Karel Drbal
- Competence Centre for Biomolecular Therapeutics Research Vienna, A-1090, Vienna
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