101
|
Oh D, Zidovska A, Xu Y, Needleman DJ. Development of time-integrated multipoint moment analysis for spatially resolved fluctuation spectroscopy with high time resolution. Biophys J 2011; 101:1546-54. [PMID: 21943437 DOI: 10.1016/j.bpj.2011.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 07/18/2011] [Accepted: 08/09/2011] [Indexed: 12/27/2022] Open
Abstract
Spatial gradients in the behaviors of soluble proteins are thought to underlie many phenomena in cell and developmental biology, but the nature and even the existence of these gradients are often unclear because few techniques can adequately characterize them. Methods with sufficient temporal resolution to study the dynamics of diffusing molecules can only sample relatively small regions, whereas methods that are capable of imaging larger areas cannot probe fast timescales. To overcome these limitations, we developed and implemented time-integrated multipoint moment analysis (TIMMA), a form of fluorescence fluctuation spectroscopy that is capable of probing timescales down to 20 μs at hundreds of different locations simultaneously in a sample. We show that TIMMA can be used to measure the diffusion of small-molecule dyes and fluorescent colloids, and that it can create spatial maps of the behavior of soluble fluorescent proteins throughout mammalian tissue culture cells. We also demonstrate that TIMMA can characterize internal gradients in the diffusion of freely moving proteins in single cells.
Collapse
Affiliation(s)
- Doogie Oh
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | | | | | | |
Collapse
|
102
|
Girard PP, Forget BC. [Light-sheet based fluorescence microscopy: the dark side of the sample finally revealed]. Med Sci (Paris) 2011; 27:753-62. [PMID: 21880264 DOI: 10.1051/medsci/2011278018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Light-sheet based fluorescence microscopy (LSM) is an optical technique that becomes more and more popular for multi-view imaging of in vivo sample in its physiological environment. LSM combines the advantages of the direct optical sectioning to the ones of optical tomography by angular scanning. In fact, a thin light-sheet illuminates laterally a section of the sample, thus limiting the effects of photobleaching and phototoxicity only to the plane of interest. The spatial resolution can be improved by combining multiple views obtained along different angle into a single data, leading to a 3D isotropic rendering of the sample. Such an approach provides several advantages in comparison to conventional 3D microscopic techniques: confocal and multiphoton microscopies. It makes LSM an optical tool suited for imaging specimens with a subcellular resolution even inside an embryo and with temporal resolution adapted for real-time monitoring of biological processes.
Collapse
|
103
|
Shedding light on the system: studying embryonic development with light sheet microscopy. Curr Opin Genet Dev 2011; 21:558-65. [PMID: 21862314 DOI: 10.1016/j.gde.2011.07.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 07/14/2011] [Accepted: 07/14/2011] [Indexed: 11/20/2022]
Abstract
Light sheet-based fluorescence microscopy (LSFM) is emerging as a powerful imaging technique for the life sciences. LSFM provides an exceptionally high imaging speed, high signal-to-noise ratio, low level of photo-bleaching and good optical penetration depth. This unique combination of capabilities makes light sheet-based microscopes highly suitable for live imaging applications. There is an outstanding potential in applying this technology to the quantitative study of embryonic development. Here, we provide an overview of the different basic implementations of LSFM, review recent technical advances in the field and highlight applications in the context of embryonic development. We conclude with a discussion of promising future directions.
Collapse
|
104
|
Capoulade J, Wachsmuth M, Hufnagel L, Knop M. Quantitative fluorescence imaging of protein diffusion and interaction in living cells. Nat Biotechnol 2011; 29:835-9. [PMID: 21822256 DOI: 10.1038/nbt.1928] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/27/2011] [Indexed: 11/09/2022]
Abstract
Diffusion processes and local dynamic equilibria inside cells lead to nonuniform spatial distributions of molecules, which are essential for processes such as nuclear organization and signaling in cell division, differentiation and migration. To understand these mechanisms, spatially resolved quantitative measurements of protein abundance, mobilities and interactions are needed, but current methods have limited capabilities to study dynamic parameters. Here we describe a microscope based on light-sheet illumination that allows massively parallel fluorescence correlation spectroscopy (FCS) measurements and use it to visualize the diffusion and interactions of proteins in mammalian cells and in isolated fly tissue. Imaging the mobility of heterochromatin protein HP1α (ref. 4) in cell nuclei we could provide high-resolution diffusion maps that reveal euchromatin areas with heterochromatin-like HP1α-chromatin interactions. We expect that FCS imaging will become a useful method for the precise characterization of cellular reaction-diffusion processes.
Collapse
Affiliation(s)
- Jérémie Capoulade
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | |
Collapse
|
105
|
Erdel F, Müller-Ott K, Baum M, Wachsmuth M, Rippe K. Dissecting chromatin interactions in living cells from protein mobility maps. Chromosome Res 2011; 19:99-115. [PMID: 20848178 DOI: 10.1007/s10577-010-9155-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The genome of eukaryotes is organized into a dynamic nucleoprotein complex referred to as chromatin, which can adopt different functional states. Both the DNA and the protein component of chromatin are subject to various post-translational modifications that define the cell's gene expression program. Their readout and establishment occurs in a spatio-temporally coordinated manner that is controlled by numerous chromatin-interacting proteins. Binding to chromatin in living cells can be measured by a spatially resolved analysis of protein mobility using fluorescence microscopy based approaches. Recent advancements in the acquisition of protein mobility data using fluorescence bleaching and correlation methods provide data sets on diffusion coefficients, binding kinetics, and cellular concentrations on different time and length scales. The combination of different techniques is needed to dissect the complex interplay of diffusive translocations, binding events, and mobility constraints of the chromatin environment. While bleaching techniques have their strength in the characterization of particles that are immobile on the second/minute time scale, a correlation analysis is advantageous to characterize transient binding events with millisecond residence time. The application and synergy effects of the different approaches to obtain protein mobility and interaction maps in the nucleus are illustrated for the analysis of heterochromatin protein 1.
Collapse
Affiliation(s)
- Fabian Erdel
- Deutsches Krebsforschungszentrum and BioQuant, Research Group Genome Organization and Function, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | | | | | | | | |
Collapse
|
106
|
Fluorescence Correlation and Cross-Correlation Spectroscopy Using Fluorescent Proteins for Measurements of Biomolecular Processes in Living Organisms. FLUORESCENT PROTEINS II 2011. [DOI: 10.1007/4243_2011_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
|
107
|
Ritter JG, Spille JH, Kaminski T, Kubitscheck U. A cylindrical zoom lens unit for adjustable optical sectioning in light sheet microscopy. BIOMEDICAL OPTICS EXPRESS 2010; 2:185-93. [PMID: 21326648 PMCID: PMC3028493 DOI: 10.1364/boe.2.000185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 12/15/2010] [Indexed: 05/26/2023]
Abstract
Light sheet microscopy became a powerful tool in life sciences. Often, however, the sheet geometry is fixed, whereas it would be advantageous to adjust the sheet geometry to specimens of different dimensions. Therefore we developed an afocal cylindrical zoom lens system comprising only 5 lenses and a total system length of less than 160 mm. Two movable optical elements were directly coupled, so that the zoom factor could be adjusted from 1x to 6.3x by a single motor. Using two different illumination objectives we achieved a light sheet thickness ranging from 2.4 µm to 36 µm corresponding to lateral fields of 54 µm to 12.3 mm, respectively. Polytene chromosomes of salivary gland cell nuclei of C.tentans larvae were imaged in vivo to demonstrate the advantages in image contrast by imaging with different light sheet dimensions.
Collapse
|
108
|
Sankaran J, Shi X, Ho LY, Stelzer EHK, Wohland T. ImFCS: a software for imaging FCS data analysis and visualization. OPTICS EXPRESS 2010; 18:25468-25481. [PMID: 21164894 DOI: 10.1364/oe.18.025468] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The multiplexing of fluorescence correlation spectroscopy (FCS), especially in imaging FCS using fast, sensitive array detectors, requires the handling of large amounts of data. One can easily collect in excess of 100,000 FCS curves a day, too many to be treated manually. Therefore, ImFCS, an open-source software which relies on standard image files was developed and provides a wide range of options for the calculation of spatial and temporal auto- and cross-correlations, as well as differences in Cross-Correlation Functions (ΔCCF). ImFCS permits fitting of standard models to correlation functions and provides optimized histograms of fitted parameters. Applications include the measurement of diffusion and flow with Imaging Total Internal Reflection FCS (ITIR-FCS) and Single Plane Illumination Microscopy FCS (SPIM-FCS) in biologically relevant samples. As a compromise between ITIR-FCS and SPIM-FCS, we extend the applications to Imaging Variable Angle-FCS (IVA-FCS) where sub-critical oblique illumination provides sample sectioning close to the cover slide.
Collapse
Affiliation(s)
- Jagadish Sankaran
- Singapore-MIT Alliance, National University of Singapore, E4-04-10, 4 Engineering Drive 3, 117576 Singapore
| | | | | | | | | |
Collapse
|
109
|
Colyer RA, Scalia G, Rech I, Gulinatti A, Ghioni M, Cova S, Weiss S, Michalet X. High-throughput FCS using an LCOS spatial light modulator and an 8 × 1 SPAD array. BIOMEDICAL OPTICS EXPRESS 2010; 1:1408-1431. [PMID: 21258559 PMCID: PMC3018120 DOI: 10.1364/boe.1.001408] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 10/14/2010] [Accepted: 11/08/2010] [Indexed: 05/05/2023]
Abstract
We present a novel approach to high-throughput Fluorescence Correlation Spectroscopy (FCS) which enables us to obtain one order of magnitude improvement in acquisition time. Our approach utilizes a liquid crystal on silicon spatial light modulator to generate dynamically adjustable focal spots, and uses an eight-pixel monolithic single-photon avalanche photodiode array. We demonstrate the capabilities of this system by showing FCS of Rhodamine 6G under various viscosities, and by showing that, with proper calibration of each detection channel, one order of magnitude improvement in acquisition speed is obtained. More generally, our approach will allow higher throughput single-molecule studies to be performed.
Collapse
Affiliation(s)
- Ryan A. Colyer
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA
| | - Giuseppe Scalia
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA
| | - Ivan Rech
- Dipartimento di Elettronica ed Informazione, Politecnico di Milano, Milano, Italy
| | - Angelo Gulinatti
- Dipartimento di Elettronica ed Informazione, Politecnico di Milano, Milano, Italy
| | - Massimo Ghioni
- Dipartimento di Elettronica ed Informazione, Politecnico di Milano, Milano, Italy
| | - Sergio Cova
- Dipartimento di Elettronica ed Informazione, Politecnico di Milano, Milano, Italy
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA
| | - Xavier Michalet
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA
| |
Collapse
|
110
|
Bestvater F, Seghiri Z, Kang MS, Gröner N, Lee JY, Im KB, Wachsmuth M. EMCCD-based spectrally resolved fluorescence correlation spectroscopy. OPTICS EXPRESS 2010; 18:23818-23828. [PMID: 21164726 DOI: 10.1364/oe.18.023818] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present an implementation of fluorescence correlation spectroscopy with spectrally resolved detection based on a combined commercial confocal laser scanning/fluorescence correlation spectroscopy microscope. We have replaced the conventional detection scheme by a prism-based spectrometer and an electron-multiplying charge-coupled device camera used to record the photons. This allows us to read out more than 80,000 full spectra per second with a signal-to-noise ratio and a quantum efficiency high enough to allow single photon counting. We can identify up to four spectrally different quantum dots in vitro and demonstrate that spectrally resolved detection can be used to characterize photophysical properties of fluorophores by measuring the spectral dependence of quantum dot fluorescence emission intermittence. Moreover, we can confirm intracellular cross-correlation results as acquired with a conventional setup and show that spectral flexibility can help to optimize the choice of the detection windows.
Collapse
Affiliation(s)
- Felix Bestvater
- Cell Biophysics Group, Institut Pasteur Korea, Sampyeong-dong 696, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | | | | | | | | | | | | |
Collapse
|
111
|
Wang X, Wohland T, Korzh V. Developing in vivo biophysics by fishing for single molecules. Dev Biol 2010; 347:1-8. [DOI: 10.1016/j.ydbio.2010.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 07/27/2010] [Accepted: 08/03/2010] [Indexed: 01/20/2023]
|