1
|
Jabloñski M, Luque GM, Gómez-Elías MD, Sanchez-Cardenas C, Xu X, de la Vega-Beltran JL, Corkidi G, Linares A, Abonza Amaro VX, Arenas-Hernandez A, Del Pilar Ramos-Godinez M, López-Saavedra A, Krapf D, Krapf D, Darszon A, Guerrero A, Buffone MG. Reorganization of the Flagellum Scaffolding Induces a Sperm Standstill During Fertilization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.22.546073. [PMID: 37904966 PMCID: PMC10614747 DOI: 10.1101/2023.06.22.546073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Mammalian sperm delve into the female reproductive tract to fertilize the female gamete. The available information about how sperm regulate their motility during the final journey to the fertilization site is extremely limited. In this work, we investigated the structural and functional changes in the sperm flagellum after AE and during the interaction with the eggs. The evidence demonstrates that the double helix actin network surrounding the mitochondrial sheath of the midpiece undergoes structural changes prior to the motility cessation. This structural modification is accompanied by a decrease in diameter of the midpiece and is driven by intracellular calcium changes that occur concomitant with a reorganization of the actin helicoidal cortex. Midpiece contraction occurs in a subset of cells that undergo AE, live-cell imaging during in vitro fertilization showed that the midpiece contraction is required for motility cessation after fusion is initiated. These findings provide the first evidence of the F-actin network's role in regulating sperm motility, adapting its function to meet specific cellular requirements during fertilization, and highlighting the broader significance of understanding sperm motility. Significant statement In this work, we demonstrate that the helical structure of polymerized actin in the flagellum undergoes a rearrangement at the time of sperm-egg fusion. This process is driven by intracellular calcium and promotes a decrease in the sperm midpiece diameter as well as the arrest in motility, which is observed after the fusion process is initiated.
Collapse
|
2
|
Lai JZ, Lin CY, Chen SJ, Cheng YM, Abe M, Lin TC, Chien FC. Temporal-Focusing Multiphoton Excitation Single-Molecule Localization Microscopy Using Spontaneously Blinking Fluorophores. Angew Chem Int Ed Engl 2024; 63:e202404942. [PMID: 38641901 DOI: 10.1002/anie.202404942] [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: 03/12/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Single-molecule localization microscopy (SMLM) based on temporal-focusing multiphoton excitation (TFMPE) and single-wavelength excitation is used to visualize the three-dimensional (3D) distribution of spontaneously blinking fluorophore-labeled subcellular structures in a thick specimen with a nanoscale-level spatial resolution. To eliminate the photobleaching effect of unlocalized molecules in out-of-focus regions for improving the utilization rate of the photon budget in 3D SMLM imaging, SMLM with single-wavelength TFMPE achieves wide-field and axially confined two-photon excitation (TPE) of spontaneously blinking fluorophores. TPE spectral measurement of blinking fluorophores is then conducted through TFMPE imaging at a tunable excitation wavelength, yielding the optimal TPE wavelength for increasing the number of detected photons from a single blinking event during SMLM. Subsequently, the TPE fluorescence of blinking fluorophores is recorded to obtain a two-dimensional TFMPE-SMLM image of the microtubules in cancer cells with a localization precision of 18±6 nm and an overall imaging resolution of approximately 51 nm, which is estimated based on the contribution of Nyquist resolution and localization precision. Combined with astigmatic imaging, the system is capable of 3D TFMPE-SMLM imaging of brain tissue section of a 5XFAD transgenic mouse with the pathological features of Alzheimer's disease, revealing the distribution of neurotoxic amyloid-beta peptide deposits.
Collapse
Affiliation(s)
- Jian-Zong Lai
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Chun-Yu Lin
- College of Photonics, National Yang Ming Chiao Tung University, No.301, Sec.2, Gaofa 3rd Rd., Guiren Dist., Tainan City, 71150, Taiwan
| | - Shean-Jen Chen
- College of Photonics, National Yang Ming Chiao Tung University, No.301, Sec.2, Gaofa 3rd Rd., Guiren Dist., Tainan City, 71150, Taiwan
| | - Yu-Min Cheng
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Manabu Abe
- Department of Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8526, Japan
| | - Tzu-Chau Lin
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Fan-Ching Chien
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| |
Collapse
|
3
|
McFadden C, Marin Z, Chen B, Daetwyler S, Wang X, Rajendran D, Dean KM, Fiolka R. Adaptive Optics in an Oblique Plane Microscope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586191. [PMID: 38562744 PMCID: PMC10983975 DOI: 10.1101/2024.03.21.586191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Adaptive optics (AO) can restore diffraction limited performance when imaging beyond superficial cell layers in vivo and in vitro, and as such is of interest for advanced 3D microscopy methods such as light-sheet fluorescence microscopy (LSFM). In a typical LSFM system, the illumination and detection paths are separate and subject to different optical aberrations. To achieve optimal microscope performance, it is necessary to sense and correct these aberrations in both light paths, resulting in a complex microscope system. Here, we show that in an oblique plane microscope (OPM), a type of LSFM with a single primary objective lens, the same deformable mirror can correct both the illumination and fluorescence detection. Besides reducing the complexity, we show that AO in OPM also restores the relative alignment of the light-sheet and focal plane, and that a projection imaging mode can stabilize and improve the wavefront correction in a sensorless AO format. We demonstrate OPM with AO on fluorescent nanospheres and by imaging the vasculature and cancer cells in zebrafish embryos embedded in a glass capillary, restoring diffraction limited resolution and improving the signal strength twofold.
Collapse
Affiliation(s)
- Conor McFadden
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Zach Marin
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Bingying Chen
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Stephan Daetwyler
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Xiaoding Wang
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Divya Rajendran
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Kevin M. Dean
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Reto Fiolka
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| |
Collapse
|
4
|
Fernando SI, Martineau JT, Hobson RJ, Vu TN, Baker B, Mueller BD, Menon R, Jorgensen EM, Gerton JM. Simultaneous spectral differentiation of multiple fluorophores in super-resolution imaging using a glass phase plate. OPTICS EXPRESS 2023; 31:33565-33581. [PMID: 37859135 PMCID: PMC10544955 DOI: 10.1364/oe.499929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/05/2023] [Accepted: 09/10/2023] [Indexed: 10/21/2023]
Abstract
By engineering the point-spread function (PSF) of single molecules, different fluorophore species can be imaged simultaneously and distinguished by their unique PSF patterns. Here, we insert a silicon-dioxide phase plate at the Fourier plane of the detection path of a wide-field fluorescence microscope to produce distinguishable PSFs (X-PSFs) at different wavelengths. We demonstrate that the resulting PSFs can be localized spatially and spectrally using a maximum-likelihood estimation algorithm and can be utilized for hyper-spectral super-resolution microscopy of biological samples. We produced superresolution images of fixed U2OS cells using X-PSFs for dSTORM imaging with simultaneous illumination of up to three fluorophore species. The species were distinguished only by the PSF pattern. We achieved ∼21-nm lateral localization precision (FWHM) and ∼17-nm axial precision (FWHM) with an average of 1,800 - 3,500 photons per PSF and a background as high as 130 - 400 photons per pixel. The modified PSF distinguished fluorescent probes with ∼80 nm separation between spectral peaks.
Collapse
Affiliation(s)
- Sanduni I. Fernando
- University of Utah Department of Physics and Astronomy, 201 James Fletcher Bldg. 115 S. 1400 E Salt Lake City, UT 84112-0830, USA
| | - Jason T. Martineau
- University of Utah Department of Physics and Astronomy, 201 James Fletcher Bldg. 115 S. 1400 E Salt Lake City, UT 84112-0830, USA
| | - Robert J. Hobson
- University of Utah School of Biological Sciences, 257 South 1400 East Salt Lake City, Utah 84112, USA
| | - Thien N. Vu
- University of Utah School of Biological Sciences, 257 South 1400 East Salt Lake City, Utah 84112, USA
| | - Brian Baker
- University of Utah Nanofab 36 S. Wasatch Drive, SMBB Room 2500 Salt Lake City, UT 84112, USA
| | - Brian D. Mueller
- University of Utah School of Biological Sciences, 257 South 1400 East Salt Lake City, Utah 84112, USA
| | - Rajesh Menon
- University of Utah Department of Electrical and Computer Engineering 50 S. Central Campus Drive, MEB Room 2110 Salt Lake City, UT 84112, USA
| | - Erik M. Jorgensen
- University of Utah School of Biological Sciences, 257 South 1400 East Salt Lake City, Utah 84112, USA
| | - Jordan M. Gerton
- University of Utah Department of Physics and Astronomy, 201 James Fletcher Bldg. 115 S. 1400 E Salt Lake City, UT 84112-0830, USA
| |
Collapse
|
5
|
Park S, Jo Y, Kang M, Hong JH, Ko S, Kim S, Park S, Park HC, Shim SH, Choi W. Label-free adaptive optics single-molecule localization microscopy for whole zebrafish. Nat Commun 2023; 14:4185. [PMID: 37443177 PMCID: PMC10344925 DOI: 10.1038/s41467-023-39896-2] [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: 10/26/2022] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Specimen-induced aberration has been a major factor limiting the imaging depth of single-molecule localization microscopy (SMLM). Here, we report the application of label-free wavefront sensing adaptive optics to SMLM for deep-tissue super-resolution imaging. The proposed system measures complex tissue aberrations from intrinsic reflectance rather than fluorescence emission and physically corrects the wavefront distortion more than three-fold stronger than the previous limit. This enables us to resolve sub-diffraction morphologies of cilia and oligodendrocytes in whole zebrafish as well as dendritic spines in thick mouse brain tissues at the depth of up to 102 μm with localization number enhancement by up to 37 times and localization precision comparable to aberration-free samples. The proposed approach can expand the application range of SMLM to whole zebrafish that cause the loss of localization number owing to severe tissue aberrations.
Collapse
Affiliation(s)
- Sanghyeon Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Republic of Korea
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Yonghyeon Jo
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Republic of Korea
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Minsu Kang
- Department of Chemistry, Korea University, Seoul, Republic of Korea
| | - Jin Hee Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Republic of Korea
| | - Sangyoon Ko
- Department of Chemistry, Korea University, Seoul, Republic of Korea
| | - Suhyun Kim
- Department of Biomedical Sciences, Korea University, Ansan, Republic of Korea
| | - Sangjun Park
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hae Chul Park
- Department of Biomedical Sciences, Korea University, Ansan, Republic of Korea
| | - Sang-Hee Shim
- Department of Chemistry, Korea University, Seoul, Republic of Korea.
| | - Wonshik Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Republic of Korea.
- Department of Physics, Korea University, Seoul, Republic of Korea.
| |
Collapse
|
6
|
Nguyen AT, Baucom DR, Wang Y, Heyes CD. Compact, Fast Blinking Cd-Free Quantum Dots for Super-Resolution Fluorescence Imaging. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:251-259. [PMID: 37388960 PMCID: PMC10302876 DOI: 10.1021/cbmi.3c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 07/01/2023]
Abstract
Quantum dots (QDs) can be used as fluorescent probes in single molecule localization microscopy to achieve subdiffraction limit resolution (super-resolution fluorescence imaging). However, the toxicity of Cd in the prototypical CdSe-based QDs can limit their use in biological applications. Furthermore, commercial CdSe QDs are usually modified with relatively thick shells of both inorganic and organic materials to render them in the 10-20 nm size range, which is relatively large for biological labels. In this report, we present compact (4-6 nm) CuInS2/ZnS (CIS/ZnS) and compare them to commercially sourced CdSe/ZnS QDs for their blinking behavior, localization precision and super-resolution imaging. Although commercial CdSe/ZnS QDs are brighter than the more compact Cd-free CIS/ZnS QD, both give comparable results of 4.5-5.0-fold improvement in imaging resolution over conventional TIRF imaging of actin filaments. This likely results from the fact that CIS/ZnS QDs show very short on-times and long off times which leads to less overlap in the point spread functions of emitting CIS/ZnS QD labels on the actin filaments at the same labeling density. These results demonstrate that CIS/ZnS QDs are an excellent candidate to complement and perhaps even replace the larger and more toxic CdSe-based QDs for robust single- molecule super-resolution imaging.
Collapse
Affiliation(s)
- Anh T. Nguyen
- Department
of Chemistry and Biochemistry, University
of Arkansas, 345 North Campus Drive, Fayetteville, Arkansas 72701, United States
| | - Dustin R. Baucom
- Department
of Chemistry and Biochemistry, University
of Arkansas, 345 North Campus Drive, Fayetteville, Arkansas 72701, United States
| | - Yong Wang
- Department
of Physics, University of Arkansas, 825 West Dickson Street, Fayetteville, Arkansas 72701, United States
| | - Colin D. Heyes
- Department
of Chemistry and Biochemistry, University
of Arkansas, 345 North Campus Drive, Fayetteville, Arkansas 72701, United States
| |
Collapse
|
7
|
Nguyen TD, Chen YI, Chen LH, Yeh HC. Recent Advances in Single-Molecule Tracking and Imaging Techniques. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:253-284. [PMID: 37314878 DOI: 10.1146/annurev-anchem-091922-073057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Since the early 1990s, single-molecule detection in solution at room temperature has enabled direct observation of single biomolecules at work in real time and under physiological conditions, providing insights into complex biological systems that the traditional ensemble methods cannot offer. In particular, recent advances in single-molecule tracking techniques allow researchers to follow individual biomolecules in their native environments for a timescale of seconds to minutes, revealing not only the distinct pathways these biomolecules take for downstream signaling but also their roles in supporting life. In this review, we discuss various single-molecule tracking and imaging techniques developed to date, with an emphasis on advanced three-dimensional (3D) tracking systems that not only achieve ultrahigh spatiotemporal resolution but also provide sufficient working depths suitable for tracking single molecules in 3D tissue models. We then summarize the observables that can be extracted from the trajectory data. Methods to perform single-molecule clustering analysis and future directions are also discussed.
Collapse
Affiliation(s)
- Trung Duc Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Limin H Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
- Texas Materials Institute, University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
8
|
Tu Z, Song C, Qin X. A numerical method for resolving finite mixtures of three-dimensional inter-site distance distributions measured by single-molecule localization microscopy. Microscopy (Oxf) 2023; 72:43-48. [PMID: 36264216 DOI: 10.1093/jmicro/dfac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/14/2022] Open
Abstract
The three-dimensional (3D) inter-site distance can be measured by single-molecule localization microscopy. Existing theories and analysis tools for 3D inter-site distance measurement only consider the simplest case where all measured distances are from an identical 3D Rician distribution. There are many problems where the 3D inter-site distance measurement result is made up of multiple components, for example, the measurement of intramolecular distances of deoxyribonucleic acid with multiple possible conformations. In these cases, the overall distance distributions become finite mixtures of 3D Rician distributions (or 3D Rician mixtures). Here, we provide a numerical method using the 3D Rician mixture model to resolve the finite 3D inter-site distance mixtures, which is based on the expectation-maximization algorithm. The proposed method has been tested on simulation data of finite 3D inter-site distance mixtures. The result using the Gaussian mixture model in the developed method is also discussed for comparison.
Collapse
Affiliation(s)
- Zhiwen Tu
- National Engineering Lab of Textile Fiber Materials & Processing Technology, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Congwei Song
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications (BIMSA), Beijing 101408, China
| | - Xianan Qin
- National Engineering Lab of Textile Fiber Materials & Processing Technology, Zhejiang Sci-Tech University, Hangzhou 310018, China.,School of Material Science and Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China.,Zhejiang Provincial Innovation Center of Advanced Textile Technology, Shaoxing 312000, China
| |
Collapse
|
9
|
Malivert M, Harms F, Veilly C, Legrand J, Li Z, Bayer E, Choquet D, Ducros M. Active image optimization for lattice light sheet microscopy in thick samples. BIOMEDICAL OPTICS EXPRESS 2022; 13:6211-6228. [PMID: 36589592 PMCID: PMC9774867 DOI: 10.1364/boe.471757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 05/02/2023]
Abstract
Lattice light-sheet microscopy (LLSM) is a very efficient technique for high resolution 3D imaging of dynamic phenomena in living biological samples. However, LLSM imaging remains limited in depth due to optical aberrations caused by sample-based refractive index mismatch. Here, we propose a simple and low-cost active image optimization (AIO) method to recover high resolution imaging inside thick biological samples. AIO is based on (1) a light-sheet autofocus step (AF) followed by (2) an adaptive optics image-based optimization. We determine the optimum AIO parameters to provide a fast, precise and robust aberration correction on biological samples. Finally, we demonstrate the performances of our approach on sub-micrometric structures in brain slices and plant roots.
Collapse
Affiliation(s)
- Maxime Malivert
- Université de Bordeaux, CNRS, INSERM, Bordeaux Imaging Center (BIC), UAR 3420, US 4, F-33000 Bordeaux, France
- Imagine Optic, F-91400 Orsay, France
| | | | | | | | - Ziqiang Li
- Université de Bordeaux, CNRS, Laboratory of Membrane Biogenesis (LBM), UMR 5200, F-33140 Villenave d’Ornon, France
| | - Emmanuelle Bayer
- Université de Bordeaux, CNRS, Laboratory of Membrane Biogenesis (LBM), UMR 5200, F-33140 Villenave d’Ornon, France
| | - Daniel Choquet
- Université de Bordeaux, CNRS, INSERM, Bordeaux Imaging Center (BIC), UAR 3420, US 4, F-33000 Bordeaux, France
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Mathieu Ducros
- Université de Bordeaux, CNRS, INSERM, Bordeaux Imaging Center (BIC), UAR 3420, US 4, F-33000 Bordeaux, France
| |
Collapse
|
10
|
Chowdhury R, Sau A, Chao J, Sharma A, Musser SM. Tuning axial and lateral localization precision in 3D super-resolution microscopy with variable astigmatism. OPTICS LETTERS 2022; 47:5727-5730. [PMID: 37219314 PMCID: PMC10332797 DOI: 10.1364/ol.466213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/06/2022] [Indexed: 05/24/2023]
Abstract
Astigmatism imaging is a three-dimensional (3D) single molecule fluorescence microscopy approach that yields super-resolved spatial information on a rapid time scale from a single image. It is ideally suited for resolving structures on a sub-micrometer scale and temporal behavior in the millisecond regime. While traditional astigmatism imaging utilizes a cylindrical lens, adaptive optics enables the astigmatism to be tuned for the experiment. We demonstrate here how the precisions in x, y, and z are inter-linked and vary with the astigmatism, z-position, and photon level. This experimentally driven and verified approach provides a guide for astigmatism selection in biological imaging strategies.
Collapse
Affiliation(s)
| | | | | | - Ankith Sharma
- Department of Cell Biology and Genetics, Texas A&M University, School of Medicine, 1114 TAMU, College Station, TX 77843, USA
| | - Siegfried M. Musser
- Department of Cell Biology and Genetics, Texas A&M University, School of Medicine, 1114 TAMU, College Station, TX 77843, USA
| |
Collapse
|
11
|
Martens KJA, Turkowyd B, Endesfelder U. Raw Data to Results: A Hands-On Introduction and Overview of Computational Analysis for Single-Molecule Localization Microscopy. FRONTIERS IN BIOINFORMATICS 2022; 1:817254. [PMID: 36303761 PMCID: PMC9580916 DOI: 10.3389/fbinf.2021.817254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/28/2021] [Indexed: 09/28/2023] Open
Abstract
Single-molecule localization microscopy (SMLM) is an advanced microscopy method that uses the blinking of fluorescent molecules to determine the position of these molecules with a resolution below the diffraction limit (∼5-40 nm). While SMLM imaging itself is becoming more popular, the computational analysis surrounding the technique is still a specialized area and often remains a "black box" for experimental researchers. Here, we provide an introduction to the required computational analysis of SMLM imaging, post-processing and typical data analysis. Importantly, user-friendly, ready-to-use and well-documented code in Python and MATLAB with exemplary data is provided as an interactive experience for the reader, as well as a starting point for further analysis. Our code is supplemented by descriptions of the computational problems and their implementation. We discuss the state of the art in computational methods and software suites used in SMLM imaging and data analysis. Finally, we give an outlook into further computational challenges in the field.
Collapse
Affiliation(s)
- Koen J. A. Martens
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States
- Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Bartosz Turkowyd
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States
- Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ulrike Endesfelder
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States
- Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| |
Collapse
|
12
|
State-of-the-Art Approaches for Image Deconvolution Problems, including Modern Deep Learning Architectures. MICROMACHINES 2021; 12:mi12121558. [PMID: 34945408 PMCID: PMC8707587 DOI: 10.3390/mi12121558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 01/06/2023]
Abstract
In modern digital microscopy, deconvolution methods are widely used to eliminate a number of image defects and increase resolution. In this review, we have divided these methods into classical, deep learning-based, and optimization-based methods. The review describes the major architectures of neural networks, such as convolutional and generative adversarial networks, autoencoders, various forms of recurrent networks, and the attention mechanism used for the deconvolution problem. Special attention is paid to deep learning as the most powerful and flexible modern approach. The review describes the major architectures of neural networks used for the deconvolution problem. We describe the difficulties in their application, such as the discrepancy between the standard loss functions and the visual content and the heterogeneity of the images. Next, we examine how to deal with this by introducing new loss functions, multiscale learning, and prior knowledge of visual content. In conclusion, a review of promising directions and further development of deconvolution methods in microscopy is given.
Collapse
|
13
|
Chen X, Liu T, Qin X, Nguyen QQ, Lee SK, Lee C, Ren Y, Chu J, Zhu G, Yoon TY, Park CY, Park H. Simultaneous Real-Time Three-Dimensional Localization and FRET Measurement of Two Distinct Particles. NANO LETTERS 2021; 21:7479-7485. [PMID: 34491760 DOI: 10.1021/acs.nanolett.1c01328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many biological processes employ mechanisms involving the locations and interactions of multiple components. Given that most biological processes occur in three dimensions, the simultaneous measurement of three-dimensional locations and interactions is necessary. However, the simultaneous three-dimensional precise localization and measurement of interactions in real time remains challenging. Here, we report a new microscopy technique to localize two spectrally distinct particles in three dimensions with an accuracy (2.35σ) of tens of nanometers with an exposure time of 100 ms and to measure their real-time interactions using fluorescence resonance energy transfer (FRET) simultaneously. Using this microscope, we tracked two distinct vesicles containing t-SNAREs or v-SNARE in three dimensions and observed FRET simultaneously during single-vesicle fusion in real time, revealing the nanoscale motion and interactions of single vesicles in vesicle fusion. Thus, this study demonstrates that our microscope can provide detailed information about real-time three-dimensional nanoscale locations, motion, and interactions in biological processes.
Collapse
Affiliation(s)
- Xingxiang Chen
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Teng Liu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xianan Qin
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Quang Quan Nguyen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Sang Kwon Lee
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Chanwoo Lee
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Yaguang Ren
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jun Chu
- Research Lab for Biomedical Optics and Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Tae-Young Yoon
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Chan Young Park
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Hyokeun Park
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| |
Collapse
|
14
|
Boka AP, Mukherjee A, Mir M. Single-molecule tracking technologies for quantifying the dynamics of gene regulation in cells, tissue and embryos. Development 2021; 148:272071. [PMID: 34490887 DOI: 10.1242/dev.199744] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
For decades, we have relied on population and time-averaged snapshots of dynamic molecular scale events to understand how genes are regulated during development and beyond. The advent of techniques to observe single-molecule kinetics in increasingly endogenous contexts, progressing from in vitro studies to living embryos, has revealed how much we have missed. Here, we provide an accessible overview of the rapidly expanding family of technologies for single-molecule tracking (SMT), with the goal of enabling the reader to critically analyse single-molecule studies, as well as to inspire the application of SMT to their own work. We start by overviewing the basics of and motivation for SMT experiments, and the trade-offs involved when optimizing parameters. We then cover key technologies, including fluorescent labelling, excitation and detection optics, localization and tracking algorithms, and data analysis. Finally, we provide a summary of selected recent applications of SMT to study the dynamics of gene regulation.
Collapse
Affiliation(s)
- Alan P Boka
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Apratim Mukherjee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mustafa Mir
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
15
|
Wang J, Zhang Y. Adaptive optics in super-resolution microscopy. BIOPHYSICS REPORTS 2021; 7:267-279. [PMID: 37287764 PMCID: PMC10233472 DOI: 10.52601/bpr.2021.210015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/23/2021] [Indexed: 06/09/2023] Open
Abstract
Fluorescence microscopy has become a routine tool in biology for interrogating life activities with minimal perturbation. While the resolution of fluorescence microscopy is in theory governed only by the diffraction of light, the resolution obtainable in practice is also constrained by the presence of optical aberrations. The past two decades have witnessed the advent of super-resolution microscopy that overcomes the diffraction barrier, enabling numerous biological investigations at the nanoscale. Adaptive optics, a technique borrowed from astronomical imaging, has been applied to correct for optical aberrations in essentially every microscopy modality, especially in super-resolution microscopy in the last decade, to restore optimal image quality and resolution. In this review, we briefly introduce the fundamental concepts of adaptive optics and the operating principles of the major super-resolution imaging techniques. We highlight some recent implementations and advances in adaptive optics for active and dynamic aberration correction in super-resolution microscopy.
Collapse
Affiliation(s)
- Jingyu Wang
- Department of Engineering Science, University of Oxford, Oxford, OX1 3PJ, UK
| | - Yongdeng Zhang
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
| |
Collapse
|
16
|
Hansen JN, Gong A, Wachten D, Pascal R, Turpin A, Jikeli JF, Kaupp UB, Alvarez L. Multifocal imaging for precise, label-free tracking of fast biological processes in 3D. Nat Commun 2021; 12:4574. [PMID: 34321468 PMCID: PMC8319204 DOI: 10.1038/s41467-021-24768-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/06/2021] [Indexed: 11/22/2022] Open
Abstract
Many biological processes happen on a nano- to millimeter scale and within milliseconds. Established methods such as confocal microscopy are suitable for precise 3D recordings but lack the temporal or spatial resolution to resolve fast 3D processes and require labeled samples. Multifocal imaging (MFI) allows high-speed 3D imaging but is limited by the compromise between high spatial resolution and large field-of-view (FOV), and the requirement for bright fluorescent labels. Here, we provide an open-source 3D reconstruction algorithm for multi-focal images that allows using MFI for fast, precise, label-free tracking spherical and filamentous structures in a large FOV and across a high depth. We characterize fluid flow and flagellar beating of human and sea urchin sperm with a z-precision of 0.15 µm, in a volume of 240 × 260 × 21 µm, and at high speed (500 Hz). The sampling volume allowed to follow sperm trajectories while simultaneously recording their flagellar beat. Our MFI concept is cost-effective, can be easily implemented, and does not rely on object labeling, which renders it broadly applicable.
Collapse
Affiliation(s)
- Jan N Hansen
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, Bonn, Germany.
| | - An Gong
- Center of Advanced European Studies and Research (caesar), Molecular Sensory Systems, Bonn, Germany
| | - Dagmar Wachten
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, Bonn, Germany
| | - René Pascal
- Center of Advanced European Studies and Research (caesar), Molecular Sensory Systems, Bonn, Germany
| | - Alex Turpin
- School of Computing Science, University of Glasgow, Glasgow, UK
| | - Jan F Jikeli
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, Bonn, Germany
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research (caesar), Molecular Sensory Systems, Bonn, Germany
- Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Luis Alvarez
- Center of Advanced European Studies and Research (caesar), Molecular Sensory Systems, Bonn, Germany.
| |
Collapse
|
17
|
Luque GM, Xu X, Romarowski A, Gervasi MG, Orta G, De la Vega-Beltrán JL, Stival C, Gilio N, Dalotto-Moreno T, Krapf D, Visconti PE, Krapf D, Darszon A, Buffone MG. Cdc42 localized in the CatSper signaling complex regulates cAMP-dependent pathways in mouse sperm. FASEB J 2021; 35:e21723. [PMID: 34224609 DOI: 10.1096/fj.202002773rr] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/11/2022]
Abstract
Sperm acquire the ability to fertilize in a process called capacitation and undergo hyperactivation, a change in the motility pattern, which depends on Ca2+ transport by CatSper channels. CatSper is essential for fertilization and it is subjected to a complex regulation that is not fully understood. Here, we report that similar to CatSper, Cdc42 distribution in the principal piece is confined to four linear domains and this localization is disrupted in CatSper1-null sperm. Cdc42 inhibition impaired CatSper activity and other Ca2+ -dependent downstream events resulting in a severe compromise of the sperm fertilizing potential. We also demonstrate that Cdc42 is essential for CatSper function by modulating cAMP production by soluble adenylate cyclase (sAC), providing a new regulatory mechanism for the stimulation of CatSper by the cAMP-dependent pathway. These results reveal a broad mechanistic insight into the regulation of Ca2+ in mammalian sperm, a matter of critical importance in male infertility as well as in contraception.
Collapse
Affiliation(s)
- Guillermina M Luque
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Xinran Xu
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO, USA
| | - Ana Romarowski
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Ciudad Autónoma de Buenos Aires, Argentina.,Department of Veterinary and Animal Science, University of Massachusetts, Amherst, MA, USA
| | - María G Gervasi
- Department of Veterinary and Animal Science, University of Massachusetts, Amherst, MA, USA
| | - Gerardo Orta
- Instituto de Biotecnología, UNAM, Cuernavaca, México
| | | | - Cintia Stival
- Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Rosario, Santa Fe, Argentina
| | - Nicolás Gilio
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Tomás Dalotto-Moreno
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Dario Krapf
- Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Rosario, Santa Fe, Argentina
| | - Pablo E Visconti
- Department of Veterinary and Animal Science, University of Massachusetts, Amherst, MA, USA
| | - Diego Krapf
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO, USA
| | | | - Mariano G Buffone
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
18
|
Single-particle tracking photoactivated localization microscopy of membrane proteins in living plant tissues. Nat Protoc 2021; 16:1600-1628. [PMID: 33627844 DOI: 10.1038/s41596-020-00471-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/24/2020] [Indexed: 01/31/2023]
Abstract
Super-resolution microscopy techniques have pushed the limit of optical imaging to unprecedented spatial resolutions. However, one of the frontiers in nanoscopy is its application to intact living organisms. Here we describe the implementation and application of super-resolution single-particle tracking photoactivated localization microscopy (sptPALM) to probe single-molecule dynamics of membrane proteins in live roots of the model plant Arabidopsis thaliana. We first discuss the advantages and limitations of sptPALM for studying the diffusion properties of membrane proteins and compare this to fluorescence recovery after photobleaching (FRAP) and fluorescence correlation spectroscopy (FCS). We describe the technical details for handling and imaging the samples for sptPALM, with a particular emphasis on the specificity of imaging plant cells, such as their thick cell walls or high degree of autofluorescence. We then provide a practical guide from data collection to image analyses. In particular, we introduce our sptPALM_viewer software and describe how to install and use it for analyzing sptPALM experiments. Finally, we report an R statistical analysis pipeline to analyze and compare sptPALM experiments. Altogether, this protocol should enable plant researchers to perform sptPALM using a benchmarked reproducible protocol. Routinely, the procedure takes 3-4 h of imaging followed by 3-4 d of image processing and data analysis.
Collapse
|
19
|
Coelho S, Baek J, Graus MS, Halstead JM, Nicovich PR, Feher K, Gandhi H, Gooding JJ, Gaus K. Ultraprecise single-molecule localization microscopy enables in situ distance measurements in intact cells. SCIENCE ADVANCES 2020; 6:eaay8271. [PMID: 32494604 PMCID: PMC7164934 DOI: 10.1126/sciadv.aay8271] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/23/2020] [Indexed: 05/24/2023]
Abstract
Single-molecule localization microscopy (SMLM) has the potential to quantify the diversity in spatial arrangements of molecules in intact cells. However, this requires that the single-molecule emitters are localized with ultrahigh precision irrespective of the sample format and the length of the data acquisition. We advance SMLM to enable direct distance measurements between molecules in intact cells on the scale between 1 and 20 nm. Our actively stabilized microscope combines three-dimensional real-time drift corrections and achieves a stabilization of <1 nm and localization precision of ~1 nm. To demonstrate the biological applicability of the new microscope, we show a 4- to 7-nm difference in spatial separations between signaling T cell receptors and phosphatases (CD45) in active and resting T cells. In summary, by overcoming the major bottlenecks in SMLM imaging, it is possible to generate molecular images with nanometer accuracy and conduct distance measurements on the biological relevant length scales.
Collapse
Affiliation(s)
- Simao Coelho
- 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, New South Wales, Australia
| | - Jongho Baek
- 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, New South Wales, Australia
| | - Matthew S. Graus
- 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, New South Wales, Australia
| | - James M. Halstead
- 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, New South Wales, Australia
| | | | - Kristen Feher
- 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, New South Wales, Australia
| | - Hetvi Gandhi
- 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, New South Wales, Australia
| | - J. Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales, 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, New South Wales, Australia
| |
Collapse
|
20
|
Siemons M, Cloin BMC, Salas DM, Nijenhuis W, Katrukha EA, Kapitein LC. Comparing strategies for deep astigmatism-based single-molecule localization microscopy. BIOMEDICAL OPTICS EXPRESS 2020; 11:735-751. [PMID: 32133221 PMCID: PMC7041481 DOI: 10.1364/boe.382023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 05/22/2023]
Abstract
Single-molecule localization microscopy (SMLM) enables fluorescent microscopy with nanometric resolution. While localizing molecules close to the coverslip is relatively straightforward using high numerical aperture (NA) oil immersion (OI) objectives, optical aberrations impede SMLM deeper in watery samples. Adaptive optics (AO) with a deformable mirror (DM) can be used to correct such aberrations and to induce precise levels of astigmatism to encode the z-position of molecules. Alternatively, the use of water immersion (WI) objectives might be sufficient to limit the most dominant aberrations. Here we compare SMLM at various depths using either WI or OI with or without AO. In addition, we compare the performance of a cylindrical lens and a DM for astigmatism-based z-encoding. We find that OI combined with adaptive optics improves localization precision beyond the performance of WI-based imaging and enables deep (>10 µm) 3D localization.
Collapse
|
21
|
Abstract
Fluorescence microscopy has long been a valuable tool for biological and medical imaging. Control of optical parameters such as the amplitude, phase, polarization and propagation angle of light gives fluorescence imaging great capabilities ranging from super-resolution imaging to long-term real-time observation of living organisms. In this review, we discuss current fluorescence imaging techniques in terms of the use of tailored or structured light for the sample illumination and fluorescence detection, providing a clear overview of their working principles and capabilities.
Collapse
Affiliation(s)
- Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Jinhan Ren
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
| |
Collapse
|
22
|
Andronov L, Ouararhni K, Stoll I, Klaholz BP, Hamiche A. CENP-A nucleosome clusters form rosette-like structures around HJURP during G1. Nat Commun 2019; 10:4436. [PMID: 31570711 PMCID: PMC6769019 DOI: 10.1038/s41467-019-12383-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/06/2019] [Indexed: 11/16/2022] Open
Abstract
CENP-A is an essential histone H3 variant that epigenetically marks the centromeric region of chromosomes. Here we show that CENP-A nucleosomes form characteristic clusters during the G1 phase of the cell cycle. 2D and 3D super-resolution microscopy and segmentation analysis reveal that these clusters encompass a globular rosette-like structure, which evolves into a more compact structure in late G1. The rosette-like clusters contain numerous CENP-A molecules and form a large cellular structure of ∼250-300 nm diameter with remarkably similar shapes for each centromere. Co-localization analysis shows that HJURP, the CENP-A chaperone, is located in the center of the rosette and serves as a nucleation point. The discovery of an HJURP-mediated CENP-A nucleation in human cells and its structural description provide important insights into the mechanism of CENP-A deposition and the organization of CENP-A chromatin in the centromeric region.
Collapse
Affiliation(s)
- Leonid Andronov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Khalid Ouararhni
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Department of Functional Genomics and Cancer, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Isabelle Stoll
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Department of Functional Genomics and Cancer, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
| | - Ali Hamiche
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
- Department of Functional Genomics and Cancer, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.
| |
Collapse
|
23
|
Lee S, Ahn S, Chakkarapani SK, Kang SH. Supersensitive Detection of the Norovirus Immunoplasmon by 3D Total Internal Reflection Scattering Defocus Microscopy with Wavelength-Dependent Transmission Grating. ACS Sens 2019; 4:2515-2523. [PMID: 31429291 DOI: 10.1021/acssensors.9b01242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Norovirus (NoV) is a major foodborne pathogen, and even low levels of virus can cause infection and gastroenteritis. We developed a supersensitive NoV sensor that detects NoV group-I capsid protein (NoVP) via three-dimensional (3D) total internal reflection scattering defocus microscopy (TIRSDM) with wavelength-dependent transmission grating (TG). The combination of evanescent wave scattering and TG significantly enhanced the detection sensitivity and selectivity of NoVP in first-order spectral images (n = +1) by minimizing spectroscopic interference and background noise. In particular, wavelength-dependent 3D defocused TG imaging (3D TG-TIRSDM) separated silver nanotag and gold nanoplate signals on a NoVP immunoplasmon chip along the x, y, and z coordinates simultaneously. Additionally, the use of wavelength-dependent TG increased the spectral resolution by 5-fold along the xy-axis and 1.4-fold along the z-axis compared to conventional 3D TIRSDM at the subdiffraction limit. The NoVP sensor exhibited a lower limit of detection of 820 yM, which is 29 000 times better than the previous potentiometer method, and a wide dynamic detection range of 820 yM to 92.45 pM (R = 0.9801). This new method could be applied to detect various pathogenic viruses during the initial stage of infection.
Collapse
|
24
|
Reymond L, Ziegler J, Knapp C, Wang FC, Huser T, Ruprecht V, Wieser S. SIMPLE: Structured illumination based point localization estimator with enhanced precision. OPTICS EXPRESS 2019; 27:24578-24590. [PMID: 31510345 DOI: 10.1364/oe.27.024578] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We present a structured illumination microscopy based point localization estimator (SIMPLE) that achieves a 2-fold increase in single molecule localization precision compared to conventional centroid estimation methods. SIMPLE advances the recently introduced MINFLUX concept by using precisely phase-shifted sinusoidal wave patterns as nanometric rulers for simultaneous particle localization based on photon count variation over a 20 μm field of view. We validate SIMPLE in silico and experimentally on a TIRF-SIM setup using a digital micro-mirror device (DMD) as a spatial light modulator.
Collapse
|
25
|
Sage D, Pham TA, Babcock H, Lukes T, Pengo T, Chao J, Velmurugan R, Herbert A, Agrawal A, Colabrese S, Wheeler A, Archetti A, Rieger B, Ober R, Hagen GM, Sibarita JB, Ries J, Henriques R, Unser M, Holden S. Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software. Nat Methods 2019; 16:387-395. [PMID: 30962624 PMCID: PMC6684258 DOI: 10.1038/s41592-019-0364-4] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 02/26/2019] [Indexed: 11/24/2022]
Abstract
With the widespread uptake of 2D and 3D single molecule localization microscopy, a large set of different data analysis packages have been developed to generate super-resolution images. In a large community effort we designed a competition to extensively characterise and rank the performance of 2D and 3D single molecule localization microscopy software packages. We generated realistic simulated datasets for popular imaging modalities - 2D, astigmatic 3D, biplane 3D, and double helix 3D - and evaluated 36 participant packages against these data. This provides the first broad assessment of 3D single molecule localization microscopy software and provides a holistic view of how the latest 2D and 3D single molecule localization software perform in realistic conditions. This resource allows researchers to identify optimal analytical software for their experiments, allows 3D SMLM software developers to benchmark new software against current state of the art, and provides insight into the current limits of the field. This study reports results from the second community-wide single molecule localization microscopy software challenge, which tested over thirty software packages on realistic simulated data for multiple popular 3D image acquisition modes as well as 2D localization microscopy.
Collapse
Affiliation(s)
- Daniel Sage
- Biomedical Imaging Group, School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Thanh-An Pham
- Biomedical Imaging Group, School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Hazen Babcock
- Harvard Center for Advanced Imaging, Harvard University, Cambridge, MA, USA
| | - Tomas Lukes
- Laboratory of Nanoscale Biology and Laboratoire d'Optique Biomédicale, STI - IBI, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Department of Radioelectronics, FEE, Czech Technical University, Prague, Czech Republic
| | - Thomas Pengo
- University of Minnesota Informatics Institute, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Jerry Chao
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA.,Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - Ramraj Velmurugan
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX, USA.,Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Alex Herbert
- MRC Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | | | - Silvia Colabrese
- Biomedical Imaging Group, School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Istituto Italiano di Tecnologia, Genova, Italy
| | - Ann Wheeler
- Advanced Imaging Resource, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Anna Archetti
- Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands
| | - Raimund Ober
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA.,Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX, USA.,Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - Guy M Hagen
- UCCS Center for the Biofrontiers Institute, University of Colorado, Colorado Springs, CO, USA
| | - Jean-Baptiste Sibarita
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France
| | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Ricardo Henriques
- Quantitative Imaging and Nanobiophysics Group, MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Michael Unser
- Biomedical Imaging Group, School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Seamus Holden
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, UK.
| |
Collapse
|
26
|
Pujals S, Feiner-Gracia N, Delcanale P, Voets I, Albertazzi L. Super-resolution microscopy as a powerful tool to study complex synthetic materials. Nat Rev Chem 2019. [DOI: 10.1038/s41570-018-0070-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
27
|
Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet 2018; 14:e1007872. [PMID: 30586358 PMCID: PMC6324821 DOI: 10.1371/journal.pgen.1007872] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/08/2019] [Accepted: 12/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chromosome organization is crucial for genome function. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase. Focusing on chromosomal regions that contribute to compartments, we discover distinct structures that, in spite of considerable variability, can predict whether such regions correspond to active (A-type) or inactive (B-type) compartments. Imaging through the depths of entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method-integrative modeling of genomic regions (IMGR)-to increase the genomic resolution of our traces to 10 kb.
Collapse
MESH Headings
- Cells, Cultured
- Chromosome Painting/methods
- Chromosome Structures/chemistry
- Chromosome Structures/genetics
- Chromosome Structures/ultrastructure
- Chromosome Walking/methods
- Chromosomes, Human, Pair 19/chemistry
- Chromosomes, Human, Pair 19/genetics
- Chromosomes, Human, Pair 19/ultrastructure
- Female
- Fluorescent Dyes
- Humans
- Imaging, Three-Dimensional
- In Situ Hybridization, Fluorescence/methods
- Male
- Models, Genetic
- Oligonucleotide Probes
- Pedigree
Collapse
Affiliation(s)
- Guy Nir
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Irene Farabella
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cynthia Pérez Estrada
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - Carl G. Ebeling
- Bruker Nano Inc., Salt Lake City, Utah, United States of America
| | - Brian J. Beliveau
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Hiroshi M. Sasaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Son C. Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shyamtanu Chattoraj
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jumana AlHaj Abed
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nuno M. C. Martins
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Huy Q. Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mohammed A. Hannan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sheikh Russell
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Neva C. Durand
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America
| | - Suhas S. P. Rao
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jocelyn Y. Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paula Soler-Vila
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | | | | | - Jeff A. Stuckey
- Bruker Nano Inc., Middleton, Wisconsin, United States of America
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, United States of America
| | - Marc A. Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - C.-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| |
Collapse
|
28
|
Abstract
In the past decades, advances in microscopy have made it possible to study the dynamics of individual biomolecules in vitro and resolve intramolecular kinetics that would otherwise be hidden in ensemble averages. More recently, single-molecule methods have been used to image, localize, and track individually labeled macromolecules in the cytoplasm of living cells, allowing investigations of intermolecular kinetics under physiologically relevant conditions. In this review, we illuminate the particular advantages of single-molecule techniques when studying kinetics in living cells and discuss solutions to specific challenges associated with these methods.
Collapse
Affiliation(s)
- Johan Elf
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden;
| | - Irmeli Barkefors
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden;
| |
Collapse
|
29
|
Kindlin-1 Regulates Epidermal Growth Factor Receptor Signaling. J Invest Dermatol 2018; 139:369-379. [PMID: 30248333 PMCID: PMC6345584 DOI: 10.1016/j.jid.2018.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 01/04/2023]
Abstract
Kindler syndrome is an autosomal recessive genodermatosis that results from mutations in the FERMT1 gene encoding t kindlin-1. Kindlin-1 localizes to focal adhesion and is known to contribute to the activation of integrin receptors. Most cases of Kindler syndrome show a reduction or complete absence of kindlin-1 in keratinocytes, resulting in defective integrin activation, cell adhesion, and migration. However, roles for kindlin-1 beyond integrin activation remain poorly defined. In this study we show that skin and keratinocytes from Kindler syndrome patients have significantly reduced expression levels of the EGFR, resulting in defective EGF-dependent signaling and cell migration. Mechanistically, we show that kindlin-1 can associate directly with EGFR in vitro and in keratinocytes in an EGF-dependent, integrin-independent manner and that formation of this complex is required for EGF-dependent migration. We further show that kindlin-1 acts to protect EGFR from lysosomal-mediated degradation. This shows a new role for kindlin-1 that has implications for understanding Kindler syndrome disease pathology.
Collapse
|
30
|
Intrinsic refractive index matched 3D dSTORM with two objectives: Comparison of detection techniques. Sci Rep 2018; 8:13343. [PMID: 30190491 PMCID: PMC6127109 DOI: 10.1038/s41598-018-31595-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 07/23/2018] [Indexed: 01/21/2023] Open
Abstract
We have built a setup for 3D single molecule localisation microscopy (SMLM) where a very high resolution is achieved by, firstly, the use of two objectives instead of one and, secondly, minimizing optical aberrations by refractive index matching with a glycerol-water mixture as immersion medium in conjunction with glycerol-immersion objectives. Multiple optical paths of the microscope allow to switch between astigmatic and interferometric localisation along the optical axis, thus enabling a direct comparison of the performance of these localisation methods.
Collapse
|
31
|
Wang Z, Cai Y, Liang Y, Dan D, Yao B, Lei M. Aberration correction method based on double-helix point spread function. JOURNAL OF BIOMEDICAL OPTICS 2018; 24:1-11. [PMID: 30182579 PMCID: PMC6975280 DOI: 10.1117/1.jbo.24.3.031005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 08/16/2018] [Indexed: 06/08/2023]
Abstract
Point spread function (PSF) engineering has met with lots of interest in various optical imaging techniques, including super-resolution microscopy, microparticle tracking, and extended depth-of-field microscopy. The intensity distributions of the modified PSFs often suffer from deteriorations caused by system aberrations, which greatly degrade the image contrast, resolution, or localization precision. We present an aberration correction method using a spiral-phase-based double-helix PSF as an aberration indicator, which is sensitive and quantitatively correlated to the spherical aberration, coma, and astigmatism. Superior to the routine iteration-based correction methods, the presented approach is iteration-free and the aberration coefficients can be directly calculated with the measured parameters, relieving the computing burden. The validity of the method is verified by both examining the intensity distribution of the conventional Gaussian PSF in three dimensions and observing muntjac skin fibroblast cells. This iteration-free correction method has a potential application in PSF engineering systems equipped with a spatial light modulator.
Collapse
Affiliation(s)
- Zhaojun Wang
- Chinese Academy of Sciences, Xi’an Institute of Optics and Precision Mechanics, State Key Laboratory of Transient Optics and Photonics, No. 17 Xinxi Road, Xi’an, Shaanxi 710119, China
- University of Chinese Academy of Sciences, No. 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yanan Cai
- Chinese Academy of Sciences, Xi’an Institute of Optics and Precision Mechanics, State Key Laboratory of Transient Optics and Photonics, No. 17 Xinxi Road, Xi’an, Shaanxi 710119, China
- University of Chinese Academy of Sciences, No. 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yansheng Liang
- Chinese Academy of Sciences, Xi’an Institute of Optics and Precision Mechanics, State Key Laboratory of Transient Optics and Photonics, No. 17 Xinxi Road, Xi’an, Shaanxi 710119, China
- University of Chinese Academy of Sciences, No. 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Dan Dan
- Chinese Academy of Sciences, Xi’an Institute of Optics and Precision Mechanics, State Key Laboratory of Transient Optics and Photonics, No. 17 Xinxi Road, Xi’an, Shaanxi 710119, China
- Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi 710049, China
| | - Baoli Yao
- Chinese Academy of Sciences, Xi’an Institute of Optics and Precision Mechanics, State Key Laboratory of Transient Optics and Photonics, No. 17 Xinxi Road, Xi’an, Shaanxi 710119, China
- Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi 710049, China
| | - Ming Lei
- Chinese Academy of Sciences, Xi’an Institute of Optics and Precision Mechanics, State Key Laboratory of Transient Optics and Photonics, No. 17 Xinxi Road, Xi’an, Shaanxi 710119, China
- Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi 710049, China
| |
Collapse
|
32
|
Niederauer C, Blumhardt P, Mücksch J, Heymann M, Lambacher A, Schwille P. Direct characterization of the evanescent field in objective-type total internal reflection fluorescence microscopy. OPTICS EXPRESS 2018; 26:20492-20506. [PMID: 30119359 DOI: 10.1364/oe.26.020492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/08/2018] [Indexed: 05/22/2023]
Abstract
Total internal reflection fluorescence (TIRF) microscopy is a commonly used method for studying fluorescently labeled molecules in close proximity to a surface. Usually, the TIRF axial excitation profile is assumed to be single-exponential with a characteristic penetration depth, governed by the incident angle of the excitation laser beam towards the optical axis. However, in practice, the excitation profile does not only comprise the theoretically predicted single-exponential evanescent field, but also an additional non-evanescent contribution, supposedly caused by scattering within the optical path or optical aberrations. We developed a calibration slide to directly characterize the TIRF excitation field. Our slide features ten height steps ranging from 25 to 550 nanometers, fabricated from a polymer with a refractive index matching that of water. Fluorophores in aqueous solution above the polymer step layers sample the excitation profile at different heights. The obtained excitation profiles confirm the theoretically predicted exponential decay over increasing step heights as well as the presence of a non-evanescent contribution.
Collapse
|
33
|
Gervasi MG, Xu X, Carbajal-Gonzalez B, Buffone MG, Visconti PE, Krapf D. The actin cytoskeleton of the mouse sperm flagellum is organized in a helical structure. J Cell Sci 2018; 131:jcs.215897. [PMID: 29739876 DOI: 10.1242/jcs.215897] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/30/2018] [Indexed: 01/08/2023] Open
Abstract
Conception in mammals is determined by the fusion of a sperm cell with an oocyte during fertilization. Motility is one of the features of sperm that allows them to succeed in fertilization, and their flagellum is essential for this function. Longitudinally, the flagellum can be divided into the midpiece, the principal piece and the end piece. A precise cytoskeletal architecture of the sperm tail is key for the acquisition of fertilization competence. It has been proposed that the actin cytoskeleton plays essential roles in the regulation of sperm motility; however, the actin organization in sperm remains elusive. In the present work, we show that there are different types of actin structures in the sperm tail by using three-dimensional stochastic optical reconstruction microscopy (STORM). In the principal piece, actin is radially distributed between the axoneme and the plasma membrane. The actin-associated proteins spectrin and adducin are also found in these structures. Strikingly, polymerized actin in the midpiece forms a double-helix that accompanies mitochondria. Our findings illustrate a novel specialized structure of actin filaments in a mammalian cell.
Collapse
Affiliation(s)
- María G Gervasi
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Xinran Xu
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Mariano G Buffone
- Instituto de Biología y Medicina Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428ADN Buenos Aires, Argentina
| | - Pablo E Visconti
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Diego Krapf
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO 80523, USA .,School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|
34
|
Abstract
Multi-colour super-resolution localization microscopy is an efficient technique to study a variety of intracellular processes, including protein-protein interactions. This technique requires specific labels that display transition between fluorescent and non-fluorescent states under given conditions. For the most commonly used label types, photoactivatable fluorescent proteins and organic fluorophores, these conditions are different, making experiments that combine both labels difficult. Here, we demonstrate that changing the standard imaging buffer of thiols/oxygen scavenging system, used for organic fluorophores, to the commercial mounting medium Vectashield increased the number of photons emitted by the fluorescent protein mEos2 and enhanced the photoconversion rate between its green and red forms. In addition, the photophysical properties of organic fluorophores remained unaltered with respect to the standard imaging buffer. The use of Vectashield together with our optimized protocol for correction of sample drift and chromatic aberrations enabled us to perform two-colour 3D super-resolution imaging of the nucleolus and resolve its three compartments.
Collapse
|
35
|
Gustavsson AK, Petrov PN, Moerner WE. Light sheet approaches for improved precision in 3D localization-based super-resolution imaging in mammalian cells [Invited]. OPTICS EXPRESS 2018; 26:13122-13147. [PMID: 29801343 PMCID: PMC6005674 DOI: 10.1364/oe.26.013122] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/30/2018] [Indexed: 05/08/2023]
Abstract
The development of imaging techniques beyond the diffraction limit has paved the way for detailed studies of nanostructures and molecular mechanisms in biological systems. Imaging thicker samples, such as mammalian cells and tissue, in all three dimensions, is challenging due to increased background and volumes to image. Light sheet illumination is a method that allows for selective irradiation of the image plane, and its inherent optical sectioning capability allows for imaging of biological samples with reduced background, photobleaching, and photodamage. In this review, we discuss the advantage of combining single-molecule imaging with light sheet illumination. We begin by describing the principles of single-molecule localization microscopy and of light sheet illumination. Finally, we present examples of designs that successfully have married single-molecule super-resolution imaging with light sheet illumination for improved precision in mammalian cells.
Collapse
|
36
|
Stival C, Ritagliati C, Xu X, Gervasi MG, Luque GM, Baró Graf C, De la Vega-Beltrán JL, Torres N, Darszon A, Krapf D, Buffone MG, Visconti PE, Krapf D. Disruption of protein kinase A localization induces acrosomal exocytosis in capacitated mouse sperm. J Biol Chem 2018; 293:9435-9447. [PMID: 29700114 DOI: 10.1074/jbc.ra118.002286] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/19/2018] [Indexed: 11/06/2022] Open
Abstract
Protein kinase A (PKA) is a broad-spectrum Ser/Thr kinase involved in the regulation of several cellular activities. Thus, its precise activation relies on being localized at specific subcellular places known as discrete PKA signalosomes. A-Kinase anchoring proteins (AKAPs) form scaffolding assemblies that play a pivotal role in PKA regulation by restricting its activity to specific microdomains. Because one of the first signaling events observed during mammalian sperm capacitation is PKA activation, understanding how PKA activity is restricted in space and time is crucial to decipher the critical steps of sperm capacitation. Here, we demonstrate that the anchoring of PKA to AKAP is not only necessary but also actively regulated during sperm capacitation. However, we find that once capacitated, the release of PKA from AKAP promotes a sudden Ca2+ influx through the sperm-specific Ca2+ channel CatSper, starting a tail-to-head Ca2+ propagation that triggers the acrosome reaction. Three-dimensional super-resolution imaging confirmed a redistribution of PKA within the flagellar structure throughout the capacitation process, which depends on anchoring to AKAP. These results represent a new signaling event that involves CatSper Ca2+ channels in the acrosome reaction, sensitive to PKA stimulation upon release from AKAP.
Collapse
Affiliation(s)
- Cintia Stival
- From the Laboratoty of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario 2000, Argentina
| | - Carla Ritagliati
- From the Laboratoty of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario 2000, Argentina
| | - Xinran Xu
- the Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523
| | - Maria G Gervasi
- the Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts 01003
| | - Guillermina M Luque
- the Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires C1428ADN, Argentina
| | - Carolina Baró Graf
- From the Laboratoty of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario 2000, Argentina
| | - José Luis De la Vega-Beltrán
- the Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos 62210, México, and
| | - Nicolas Torres
- the Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires C1428ADN, Argentina
| | - Alberto Darszon
- the Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos 62210, México, and
| | - Diego Krapf
- the Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523.,the School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523
| | - Mariano G Buffone
- the Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires C1428ADN, Argentina
| | - Pablo E Visconti
- the Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts 01003
| | - Dario Krapf
- From the Laboratoty of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario 2000, Argentina,
| |
Collapse
|
37
|
Miller H, Zhou Z, Shepherd J, Wollman AJM, Leake MC. Single-molecule techniques in biophysics: a review of the progress in methods and applications. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:024601. [PMID: 28869217 DOI: 10.1088/1361-6633/aa8a02] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.
Collapse
Affiliation(s)
- Helen Miller
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom
| | | | | | | | | |
Collapse
|
38
|
Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. The 4D nucleome project. Nature 2018; 549:219-226. [PMID: 28905911 DOI: 10.1038/nature23884] [Citation(s) in RCA: 427] [Impact Index Per Article: 71.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/27/2017] [Indexed: 12/19/2022]
Abstract
The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells.
Collapse
Affiliation(s)
- Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Howard Hughes Medical Institute, Worcester, Massachusetts 01605, USA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Victor O Leshyk
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, New York 10027, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Clodagh C O'Shea
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, University of California San Diego, La Jolla California 92093, USA
| | - Joan C Ritland Politz
- Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Howard Hughes Medical Institute, Seattle, Washington 98109, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | | |
Collapse
|
39
|
Cabriel C, Bourg N, Dupuis G, Lévêque-Fort S. Aberration-accounting calibration for 3D single-molecule localization microscopy. OPTICS LETTERS 2018; 43:174-177. [PMID: 29328231 DOI: 10.1364/ol.43.000174] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/03/2017] [Indexed: 05/17/2023]
Abstract
We propose a straightforward sample-based technique to calibrate the axial detection in 3D single-molecule localization microscopy. Using microspheres coated with fluorescent molecules, the calibration curves of point spread function-shaping or intensity-based measurements can be obtained over the imaging depth range. This experimental method takes into account the effect of the spherical aberration without requiring computational correction. We demonstrate its efficiency for astigmatic imaging in a 1.2 μm range above the coverslip.
Collapse
|
40
|
Angular reconstitution-based 3D reconstructions of nanomolecular structures from superresolution light-microscopy images. Proc Natl Acad Sci U S A 2017; 114:9273-9278. [PMID: 28811371 DOI: 10.1073/pnas.1704908114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Superresolution light microscopy allows the imaging of labeled supramolecular assemblies at a resolution surpassing the classical diffraction limit. A serious limitation of the superresolution approach is sample heterogeneity and the stochastic character of the labeling procedure. To increase the reproducibility and the resolution of the superresolution results, we apply multivariate statistical analysis methods and 3D reconstruction approaches originally developed for cryogenic electron microscopy of single particles. These methods allow for the reference-free 3D reconstruction of nanomolecular structures from two-dimensional superresolution projection images. Since these 2D projection images all show the structure in high-resolution directions of the optical microscope, the resulting 3D reconstructions have the best possible isotropic resolution in all directions.
Collapse
|
41
|
McGorty R, Xie D, Huang B. High-NA open-top selective-plane illumination microscopy for biological imaging. OPTICS EXPRESS 2017; 25:17798-17810. [PMID: 28789271 PMCID: PMC5557333 DOI: 10.1364/oe.25.017798] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Selective-plane illumination microscopy (SPIM) provides unparalleled advantages for the volumetric imaging of living organisms over extended times. However, the spatial configuration of a SPIM system often limits its compatibility with many widely used biological sample holders such as multi-well chambers and plates. To solve this problem, we developed a high numerical aperture (NA) open-top configuration that places both the excitation and detection objectives on the opposite of the sample coverglass. We carried out a theoretical calculation to analyze the structure of the system-induced aberrations. We then experimentally compensated the system aberrations using adaptive optics combined with static optical components, demonstrating near-diffraction-limited performance in imaging fluorescently labeled cells.
Collapse
Affiliation(s)
- Ryan McGorty
- Dept. of Physics and Biophysics, University of San Diego, CA 92110,
USA
| | - Dan Xie
- Dept. of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158,
USA
| | - Bo Huang
- Dept. of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158,
USA
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158,
USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158,
USA
| |
Collapse
|
42
|
Lee A, Tsekouras K, Calderon C, Bustamante C, Pressé S. Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis. Chem Rev 2017; 117:7276-7330. [PMID: 28414216 PMCID: PMC5487374 DOI: 10.1021/acs.chemrev.6b00729] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Super-resolution microscopy provides direct insight into fundamental biological processes occurring at length scales smaller than light's diffraction limit. The analysis of data at such scales has brought statistical and machine learning methods into the mainstream. Here we provide a survey of data analysis methods starting from an overview of basic statistical techniques underlying the analysis of super-resolution and, more broadly, imaging data. We subsequently break down the analysis of super-resolution data into four problems: the localization problem, the counting problem, the linking problem, and what we've termed the interpretation problem.
Collapse
Affiliation(s)
- Antony Lee
- Department of Physics, University of California at Berkeley, Berkeley, California 94720, United States
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California at Berkeley, Berkeley, California 94720, United States
| | - Konstantinos Tsekouras
- Department of Physics, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | | | - Carlos Bustamante
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California at Berkeley, Berkeley, California 94720, United States
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, United States
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, United States
- Kavli Energy Nanosciences Institute, University of California at Berkeley, Berkeley, California 94720, United States
| | - Steve Pressé
- Department of Physics, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
- Department of Cell and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| |
Collapse
|
43
|
von Diezmann A, Shechtman Y, Moerner WE. Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking. Chem Rev 2017; 117:7244-7275. [PMID: 28151646 PMCID: PMC5471132 DOI: 10.1021/acs.chemrev.6b00629] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-molecule super-resolution fluorescence microscopy and single-particle tracking are two imaging modalities that illuminate the properties of cells and materials on spatial scales down to tens of nanometers or with dynamical information about nanoscale particle motion in the millisecond range, respectively. These methods generally use wide-field microscopes and two-dimensional camera detectors to localize molecules to much higher precision than the diffraction limit. Given the limited total photons available from each single-molecule label, both modalities require careful mathematical analysis and image processing. Much more information can be obtained about the system under study by extending to three-dimensional (3D) single-molecule localization: without this capability, visualization of structures or motions extending in the axial direction can easily be missed or confused, compromising scientific understanding. A variety of methods for obtaining both 3D super-resolution images and 3D tracking information have been devised, each with their own strengths and weaknesses. These include imaging of multiple focal planes, point-spread-function engineering, and interferometric detection. These methods may be compared based on their ability to provide accurate and precise position information on single-molecule emitters with limited photons. To successfully apply and further develop these methods, it is essential to consider many practical concerns, including the effects of optical aberrations, field dependence in the imaging system, fluorophore labeling density, and registration between different color channels. Selected examples of 3D super-resolution imaging and tracking are described for illustration from a variety of biological contexts and with a variety of methods, demonstrating the power of 3D localization for understanding complex systems.
Collapse
Affiliation(s)
| | - Yoav Shechtman
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
| |
Collapse
|
44
|
Petrov PN, Shechtman Y, Moerner WE. Measurement-based estimation of global pupil functions in 3D localization microscopy. OPTICS EXPRESS 2017; 25:7945-7959. [PMID: 28380911 PMCID: PMC5810908 DOI: 10.1364/oe.25.007945] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We report the use of a phase retrieval procedure based on maximum likelihood estimation (MLE) to produce an improved, experimentally calibrated model of a point spread function (PSF) for use in three-dimensional (3D) localization microscopy experiments. The method estimates a global pupil phase function (which includes both the PSF and system aberrations) over the full axial range from a simple calibration scan. The pupil function is used to refine the PSF model and hence enable superior localizations from experimental data. To demonstrate the utility of the procedure, we apply it to experimental data acquired with a microscope employing a tetrapod PSF with a 6 µm axial range. The phase-retrieved model demonstrates significant improvements in both accuracy and precision of 3D localizations relative to the model based on scalar diffraction theory. The localization precision of the phase-retrieved model is shown to be near the limits imposed by estimation theory, and the reproducibility of the procedure is characterized and discussed. Code which performs the phase retrieval algorithm is provided.
Collapse
Affiliation(s)
- Petar N. Petrov
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305, USA
| | - Yoav Shechtman
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305, USA
- Present address: Department of Biomedical Engineering, Technion−Israel Institute of Technology, Haifa 32000, Israel
| | - W. E. Moerner
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305, USA
| |
Collapse
|
45
|
Adaptive optical fluorescence microscopy. Nat Methods 2017; 14:374-380. [DOI: 10.1038/nmeth.4218] [Citation(s) in RCA: 295] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/06/2017] [Indexed: 12/24/2022]
|
46
|
Tafteh R, Abraham L, Seo D, Lu HY, Gold MR, Chou KC. Real-time 3D stabilization of a super-resolution microscope using an electrically tunable lens. OPTICS EXPRESS 2016; 24:22959-22970. [PMID: 27828362 DOI: 10.1364/oe.24.022959] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single-molecule localization microscopy (SMLM) has become an essential tool for examining a wide variety of biological structures and processes. However, the relatively long acquisition time makes SMLM prone to drift-induced artifacts. Here we report an optical design with an electrically tunable lens (ETL) that actively stabilizes a SMLM in three dimensions and nearly eliminates the mechanical drift (RMS ~0.7 nm lateral and ~2.7 nm axial). The bifocal design that employed fiducial markers on the coverslip was able to stabilize the sample regardless of the imaging depth. The effectiveness of the ETL was demonstrated by imaging endosomal transferrin receptors near the apical surface of B-lymphocytes at a depth of 8 µm. The drift-free images obtained with the stabilization system showed that the transferrin receptors were present in distinct but heterogeneous clusters with a bimodal size distribution. In contrast, the images obtained without the stabilization system showed a broader unimodal size distribution. Thus, this stabilization system enables a more accurate analysis of cluster topology. Additionally, this ETL-based stabilization system is cost-effective and can be integrated into existing microscopy systems.
Collapse
|
47
|
Zhang P, Kim K, Lee S, Chakkarapani SK, Fang N, Kang SH. Augmented 3D super-resolution of fluorescence-free nanoparticles using enhanced dark-field illumination based on wavelength-modulation and a least-cubic algorithm. Sci Rep 2016; 6:32863. [PMID: 27619347 PMCID: PMC5020655 DOI: 10.1038/srep32863] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/16/2016] [Indexed: 12/19/2022] Open
Abstract
Augmented three-dimensional (3D) subdiffraction-limited resolution of fluorescence-free single-nanoparticles was achieved with wavelength-dependent enhanced dark-field (EDF) illumination and a least-cubic algorithm. Various plasmonic nanoparticles on a glass slide (i.e., gold nanoparticles, GNPs; silver nanoparticles, SNPs; and gold nanorods, GNRs) were imaged and sliced in the z-direction to a thickness of 10 nm. Single-particle images were then compared with simulation data. The 3D coordinates of individual GNP, SNP, and GNR nanoparticles (x, y, z) were resolved by fitting the data with 3D point spread functions using a least-cubic algorithm and collation. Final, 3D super-resolution microscopy (SRM) images were obtained by resolving 3D coordinates and their Cramér-Rao lower bound-based localization precisions in an image space (530 nm × 530 nm × 300 nm) with a specific voxel size (2.5 nm × 2.5 nm × 5 nm). Compared with the commonly used least-square method, the least-cubic method was more useful for finding the center in asymmetric cases (i.e., nanorods) with high precision and accuracy. This novel 3D fluorescence-free SRM technique was successfully applied to resolve the positions of various nanoparticles on glass and gold nanospots (in vitro) as well as in a living single cell (in vivo) with subdiffraction limited resolution in 3D.
Collapse
Affiliation(s)
- Peng Zhang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Kyungsoo Kim
- Department of Applied Mathematics, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Suresh Kumar Chakkarapani
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Ning Fang
- Department of Chemistry, Georgia State University, 308 Petit Science Center, Atlanta, GA 30303, USA
| | - Seong Ho Kang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.,Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| |
Collapse
|
48
|
Sokoll S, Prokazov Y, Hanses M, Biermann B, Tönnies K, Heine M. Fast Three-Dimensional Single-Particle Tracking in Natural Brain Tissue. Biophys J 2016; 109:1463-71. [PMID: 26445447 DOI: 10.1016/j.bpj.2015.07.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/15/2015] [Accepted: 07/31/2015] [Indexed: 11/18/2022] Open
Abstract
Observation of molecular dynamics is often biased by the optical very heterogeneous environment of cells and complex tissue. Here, we have designed an algorithm that facilitates molecular dynamic analyses within brain slices. We adjust fast astigmatism-based three-dimensional single-particle tracking techniques to depth-dependent optical aberrations induced by the refractive index mismatch so that they are applicable to complex samples. In contrast to existing techniques, our online calibration method determines the aberration directly from the acquired two-dimensional image stream by exploiting the inherent particle movement and the redundancy introduced by the astigmatism. The method improves the positioning by reducing the systematic errors introduced by the aberrations, and allows correct derivation of the cellular morphology and molecular diffusion parameters in three dimensions independently of the imaging depth. No additional experimental effort for the user is required. Our method will be useful for many imaging configurations, which allow imaging in deep cellular structures.
Collapse
Affiliation(s)
- Stefan Sokoll
- Research Group for Molecular Physiology, Leibniz Institute for Neurobiology, Magdeburg, Germany; Research Group for Image Processing and Pattern Recognition, Otto-von-Guericke University, Magdeburg, Germany
| | - Yury Prokazov
- Special Lab for Electron and Laserscanning Microscopy, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Magnus Hanses
- Research Group for Molecular Physiology, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Barbara Biermann
- Research Group for Molecular Physiology, Leibniz Institute for Neurobiology, Magdeburg, Germany; Institute of Neural and Sensory Physiology, Medical Faculty, University of Düsseldorf, Germany
| | - Klaus Tönnies
- Research Group for Image Processing and Pattern Recognition, Otto-von-Guericke University, Magdeburg, Germany
| | - Martin Heine
- Research Group for Molecular Physiology, Leibniz Institute for Neurobiology, Magdeburg, Germany.
| |
Collapse
|
49
|
Liu C, Liu YL, Perillo EP, Dunn AK, Yeh HC. Single-Molecule Tracking and Its Application in Biomolecular Binding Detection. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2016; 22:6804013. [PMID: 27660404 PMCID: PMC5028128 DOI: 10.1109/jstqe.2016.2568160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In the past two decades significant advances have been made in single-molecule detection, which enables the direct observation of single biomolecules at work in real time and under physiological conditions. In particular, the development of single-molecule tracking (SMT) microscopy allows us to monitor the motion paths of individual biomolecules in living systems, unveiling the localization dynamics and transport modalities of the biomolecules that support the development of life. Beyond the capabilities of traditional camera-based tracking techniques, state-of-the-art SMT microscopies developed in recent years can record fluorescence lifetime while tracking a single molecule in the 3D space. This multiparameter detection capability can open the door to a wide range of investigations at the cellular or tissue level, including identification of molecular interaction hotspots and characterization of association/dissociation kinetics between molecules. In this review, we discuss various SMT techniques developed to date, with an emphasis on our recent development of the next generation 3D tracking system that not only achieves ultrahigh spatiotemporal resolution but also provides sufficient working depth suitable for live animal imaging. We also discuss the challenges that current SMT techniques are facing and the potential strategies to tackle those challenges.
Collapse
Affiliation(s)
- Cong Liu
- University of Texas at Austin, Austin, TX 78703 USA
| | | | | | | | | |
Collapse
|
50
|
Oudjedi L, Fiche JB, Abrahamsson S, Mazenq L, Lecestre A, Calmon PF, Cerf A, Nöllmann M. Astigmatic multifocus microscopy enables deep 3D super-resolved imaging. BIOMEDICAL OPTICS EXPRESS 2016; 7:2163-73. [PMID: 27375935 PMCID: PMC4918573 DOI: 10.1364/boe.7.002163] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/22/2016] [Accepted: 03/17/2016] [Indexed: 05/15/2023]
Abstract
We have developed a 3D super-resolution microscopy method that enables deep imaging in cells. This technique relies on the effective combination of multifocus microscopy and astigmatic 3D single-molecule localization microscopy. We describe the optical system and the fabrication process of its key element, the multifocus grating. Then, two strategies for localizing emitters with our imaging method are presented and compared with a previously described deep 3D localization algorithm. Finally, we demonstrate the performance of the method by imaging the nuclear envelope of eukaryotic cells reaching a depth of field of ~4µm.
Collapse
Affiliation(s)
- Laura Oudjedi
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Sara Abrahamsson
- Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Laurent Mazenq
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Aurélie Lecestre
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Pierre-François Calmon
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Aline Cerf
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Marcelo Nöllmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| |
Collapse
|