1
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Chareyre S, Li X, Anjuwon-Foster BR, Updegrove TB, Clifford S, Brogan AP, Su Y, Zhang L, Chen J, Shroff H, Ramamurthi KS. Cell division machinery drives cell-specific gene activation during differentiation in Bacillus subtilis. Proc Natl Acad Sci U S A 2024; 121:e2400584121. [PMID: 38502707 PMCID: PMC10990147 DOI: 10.1073/pnas.2400584121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024] Open
Abstract
When faced with starvation, the bacterium Bacillus subtilis transforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components FtsA and FtsZ, after which the sigma factor σF is exclusively activated in the smaller daughter cell. Compartment-specific activation of σF requires the SpoIIE phosphatase, which displays a biased localization on one side of the asymmetric division septum and associates with the structural protein DivIVA, but the mechanism by which this preferential localization is achieved is unclear. Here, we isolated a variant of DivIVA that indiscriminately activates σF in both daughter cells due to promiscuous localization of SpoIIE, which was corrected by overproduction of FtsA and FtsZ. We propose that the core components of the redeployed cell division machinery drive the asymmetric localization of DivIVA and SpoIIE to trigger the initiation of the sporulation program.
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Affiliation(s)
- Sylvia Chareyre
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Xuesong Li
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD20892
- HHMI, Ashburn, VA20147
| | | | - Taylor B. Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Sarah Clifford
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Anna P. Brogan
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD20892
- HHMI, Ashburn, VA20147
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, NIH, Bethesda, MD20892
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, NIH, Bethesda, MD20892
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD20892
- HHMI, Ashburn, VA20147
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2
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Shroff H, Testa I, Jug F, Manley S. Live-cell imaging powered by computation. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00702-6. [PMID: 38378991 DOI: 10.1038/s41580-024-00702-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preserving cell viability. Computational methods can help to address this challenge and are now shifting the boundaries of what is possible to capture in living systems. In this Review, we discuss these computational methods focusing on artificial intelligence-based approaches that can be layered on top of commonly used existing microscopies as well as hybrid methods that integrate computation and microscope hardware. We specifically discuss how computational approaches can improve the signal-to-noise ratio, spatial resolution, temporal resolution and multi-colour capacity of live-cell imaging.
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Affiliation(s)
- Hari Shroff
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Florian Jug
- Fondazione Human Technopole (HT), Milan, Italy
| | - Suliana Manley
- Institute of Physics, School of Basic Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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3
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Johnson C, Guo M, Schneider MC, Su Y, Khuon S, Reiser N, Wu Y, La Riviere P, Shroff H. Phase diversity-based wavefront sensing for fluorescence microscopy. bioRxiv 2024:2023.12.19.572369. [PMID: 38168170 PMCID: PMC10760184 DOI: 10.1101/2023.12.19.572369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Fluorescence microscopy is an invaluable tool in biology, yet its performance is compromised when the wavefront of light is distorted due to optical imperfections or the refractile nature of the sample. Such optical aberrations can dramatically lower the information content of images by degrading image contrast, resolution, and signal. Adaptive optics (AO) methods can sense and subsequently cancel the aberrated wavefront, but are too complex, inefficient, slow, or expensive for routine adoption by most labs. Here we introduce a rapid, sensitive, and robust wavefront sensing scheme based on phase diversity, a method successfully deployed in astronomy but underused in microscopy. Our method enables accurate wavefront sensing to less than λ/35 root mean square (RMS) error with few measurements, and AO with no additional hardware besides a corrective element. After validating the method with simulations, we demonstrate calibration of a deformable mirror > 100-fold faster than comparable methods (corresponding to wavefront sensing on the ~100 ms scale), and sensing and subsequent correction of severe aberrations (RMS wavefront distortion exceeding λ/2), restoring diffraction-limited imaging on extended biological samples.
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Affiliation(s)
- Courtney Johnson
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Min Guo
- Current address: State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Yijun Su
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Satya Khuon
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Nikolaj Reiser
- Department of Radiology, University of Chicago, Chicago, IL, USA
| | - Yicong Wu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Patrick La Riviere
- Department of Radiology, University of Chicago, Chicago, IL, USA
- MBL Fellows Program, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Hari Shroff
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- MBL Fellows Program, Marine Biological Laboratory, Woods Hole, MA, USA
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4
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Sadhu RK, Hernandez-Padilla C, Eisenbach YE, Penič S, Zhang L, Vishwasrao HD, Behkam B, Konstantopoulos K, Shroff H, Iglič A, Peles E, Nain AS, Gov NS. Author Correction: Experimental and theoretical model for the origin of coiling of cellular protrusions around fibers. Nat Commun 2023; 14:8518. [PMID: 38129398 PMCID: PMC10739969 DOI: 10.1038/s41467-023-44423-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Affiliation(s)
- Raj Kumar Sadhu
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
- Institut Curie, PSL Research University, CNRS, UMR 168, Paris, France.
| | | | - Yael Eshed Eisenbach
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Samo Penič
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Bahareh Behkam
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | | | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Aleš Iglič
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Elior Peles
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Amrinder S Nain
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Nir S Gov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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5
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Guo M, Wu Y, Su Y, Qian S, Krueger E, Christensen R, Kroeschell G, Bui J, Chaw M, Zhang L, Liu J, Hou X, Han X, Ma X, Zhovmer A, Combs C, Moyle M, Yemini E, Liu H, Liu Z, La Riviere P, Colón-Ramos D, Shroff H. Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy. bioRxiv 2023:2023.10.15.562439. [PMID: 37986950 PMCID: PMC10659418 DOI: 10.1101/2023.10.15.562439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Optical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing image acquisition, applying additional dose, or introducing more optics into the imaging path. Our method (i) introduces synthetic aberrations to images acquired on the shallow side of image stacks, making them resemble those acquired deeper into the volume and (ii) trains neural networks to reverse the effect of these aberrations. We use simulations to show that applying the trained 'de-aberration' networks outperforms alternative methods, and subsequently apply the networks to diverse datasets captured with confocal, light-sheet, multi-photon, and super-resolution microscopy. In all cases, the improved quality of the restored data facilitates qualitative image inspection and improves downstream image quantitation, including orientational analysis of blood vessels in mouse tissue and improved membrane and nuclear segmentation in C. elegans embryos.
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Affiliation(s)
- Min Guo
- Current address: State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Yicong Wu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, Maryland, USA
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, Maryland, USA
| | - Shuhao Qian
- Current address: State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Eric Krueger
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Grant Kroeschell
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Johnny Bui
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Matthew Chaw
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, Maryland, USA
| | - Jiamin Liu
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, Maryland, USA
| | - Xuekai Hou
- Current address: State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xiaofei Han
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Xuefei Ma
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Alexander Zhovmer
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Christian Combs
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, MD, USA
| | - Mark Moyle
- Department of Biology, Brigham Young University-Idaho, Rexburg, ID, USA
| | - Eviatar Yemini
- Department of Neurobiology, UMass Chan Medical School, Worcester, MA
| | - Huafeng Liu
- Current address: State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Zhiyi Liu
- Current address: State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Patrick La Riviere
- Department of Radiology, University of Chicago, Chicago, IL, USA
- MBL Fellows Program, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Daniel Colón-Ramos
- MBL Fellows Program, Marine Biological Laboratory, Woods Hole, MA, USA
- Wu Tsai Institute, Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, Maryland, USA
- MBL Fellows Program, Marine Biological Laboratory, Woods Hole, MA, USA
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6
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Sadhu RK, Hernandez-Padilla C, Eisenbach YE, Penič S, Zhang L, Vishwasrao HD, Behkam B, Konstantopoulos K, Shroff H, Iglič A, Peles E, Nain AS, Gov NS. Experimental and theoretical model for the origin of coiling of cellular protrusions around fibers. Nat Commun 2023; 14:5612. [PMID: 37699891 PMCID: PMC10497540 DOI: 10.1038/s41467-023-41273-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/29/2023] [Indexed: 09/14/2023] Open
Abstract
Protrusions at the leading-edge of a cell play an important role in sensing the extracellular cues during cellular spreading and motility. Recent studies provided indications that these protrusions wrap (coil) around the extracellular fibers. However, the physics of this coiling process, and the mechanisms that drive it, are not well understood. We present a combined theoretical and experimental study of the coiling of cellular protrusions on fibers of different geometry. Our theoretical model describes membrane protrusions that are produced by curved membrane proteins that recruit the protrusive forces of actin polymerization, and identifies the role of bending and adhesion energies in orienting the leading-edges of the protrusions along the azimuthal (coiling) direction. Our model predicts that the cell's leading-edge coils on fibers with circular cross-section (above some critical radius), but the coiling ceases for flattened fibers of highly elliptical cross-section. These predictions are verified by 3D visualization and quantitation of coiling on suspended fibers using Dual-View light-sheet microscopy (diSPIM). Overall, we provide a theoretical framework, supported by experiments, which explains the physical origin of the coiling phenomenon.
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Affiliation(s)
- Raj Kumar Sadhu
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
- Institut Curie, PSL Research University, CNRS, UMR 168, Paris, France.
| | | | - Yael Eshed Eisenbach
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Samo Penič
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Bahareh Behkam
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | | | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Aleš Iglič
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Elior Peles
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Amrinder S Nain
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Nir S Gov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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7
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Li X, Wu Y, Su Y, Rey-Suarez I, Matthaeus C, Updegrove TB, Wei Z, Zhang L, Sasaki H, Li Y, Guo M, Giannini JP, Vishwasrao HD, Chen J, Lee SJJ, Shao L, Liu H, Ramamurthi KS, Taraska JW, Upadhyaya A, La Riviere P, Shroff H. Three-dimensional structured illumination microscopy with enhanced axial resolution. Nat Biotechnol 2023; 41:1307-1319. [PMID: 36702897 PMCID: PMC10497409 DOI: 10.1038/s41587-022-01651-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/16/2022] [Indexed: 01/27/2023]
Abstract
The axial resolution of three-dimensional structured illumination microscopy (3D SIM) is limited to ∼300 nm. Here we present two distinct, complementary methods to improve axial resolution in 3D SIM with minimal or no modification to the optical system. We show that placing a mirror directly opposite the sample enables four-beam interference with higher spatial frequency content than 3D SIM illumination, offering near-isotropic imaging with ∼120-nm lateral and 160-nm axial resolution. We also developed a deep learning method achieving ∼120-nm isotropic resolution. This method can be combined with denoising to facilitate volumetric imaging spanning dozens of timepoints. We demonstrate the potential of these advances by imaging a variety of cellular samples, delineating the nanoscale distribution of vimentin and microtubule filaments, observing the relative positions of caveolar coat proteins and lysosomal markers and visualizing cytoskeletal dynamics within T cells in the early stages of immune synapse formation.
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Affiliation(s)
- Xuesong Li
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA.
| | - Yicong Wu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA.
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Leica Microsystems, Inc., Deerfield, IL, USA
- SVision, LLC, Bellevue, WA, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Ivan Rey-Suarez
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Claudia Matthaeus
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Taylor B Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhuang Wei
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Hideki Sasaki
- Leica Microsystems, Inc., Deerfield, IL, USA
- SVision, LLC, Bellevue, WA, USA
| | - Yue Li
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Min Guo
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - John P Giannini
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Shih-Jong J Lee
- Leica Microsystems, Inc., Deerfield, IL, USA
- SVision, LLC, Bellevue, WA, USA
| | - Lin Shao
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Huafeng Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arpita Upadhyaya
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
| | - Patrick La Riviere
- Department of Radiology, University of Chicago, Chicago, IL, USA
- MBL Fellows, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- MBL Fellows, Marine Biological Laboratory, Woods Hole, MA, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
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8
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Chareyre S, Li X, Anjuwon-Foster BR, Clifford S, Brogan A, Su Y, Shroff H, Ramamurthi KS. Cell division machinery drives cell-specific gene activation during bacterial differentiation. bioRxiv 2023:2023.08.10.552768. [PMID: 37790399 PMCID: PMC10542145 DOI: 10.1101/2023.08.10.552768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
When faced with starvation, the bacterium Bacillus subtilis transforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components FtsA and FtsZ, after which the sigma factor σF is exclusively activated in the smaller daughter cell. Compartment specific activation of σF requires the SpoIIE phosphatase, which displays a biased localization on one side of the asymmetric division septum and associates with the structural protein DivIVA, but the mechanism by which this preferential localization is achieved is unclear. Here, we isolated a variant of DivIVA that indiscriminately activates σF in both daughter cells due to promiscuous localization of SpoIIE, which was corrected by overproduction of FtsA and FtsZ. We propose that a unique feature of the sporulation septum, defined by the cell division machinery, drives the asymmetric localization of DivIVA and SpoIIE to trigger the initiation of the sporulation program.
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Affiliation(s)
- Sylvia Chareyre
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xuesong Li
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Brandon R Anjuwon-Foster
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sarah Clifford
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anna Brogan
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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9
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Reiser N, Guo M, Shroff H, Riviere PJL. Phase Diverse Phase Retrieval for Microscopy: Comparison of Gaussian and Poisson Approaches. ArXiv 2023:arXiv:2308.00734v1. [PMID: 37791105 PMCID: PMC10543013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Phase diversity is a widefield aberration correction method that uses multiple images to estimate the phase aberration at the pupil plane of an imaging system by solving an optimization problem. This estimated aberration can then be used to deconvolve the aberrated image or to reacquire it with aberration corrections applied to a deformable mirror. The optimization problem for aberration estimation has been formulated for both Gaussian and Poisson noise models but the Poisson model has never been studied in microscopy nor compared with the Gaussian model. Here, the Gaussian- and Poisson-based estimation algorithms are implemented and compared for widefield microscopy in simulation. The Poisson algorithm is found to match or outperform the Gaussian algorithm in a variety of situations, and converges in a similar or decreased amount of time. The Gaussian algorithm does perform better in low-light regimes when image noise is dominated by additive Gaussian noise. The Poisson algorithm is also found to be more robust to the effects of spatially variant aberration and phase noise. Finally, the relative advantages of re-acquisition with aberration correction and deconvolution with aberrated point spread functions are compared.
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10
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Ngo TB, DeStefano S, Liu J, Su Y, Shroff H, Vishwasrao HD, Sadtler K. Label-free cleared tissue microscopy and machine learning for 3D histopathology of biomaterial implants. J Biomed Mater Res A 2023; 111:840-850. [PMID: 36861434 DOI: 10.1002/jbm.a.37515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 02/08/2023] [Indexed: 03/03/2023]
Abstract
Tissue clearing of whole intact organs has enhanced imaging by enabling the exploration of tissue structure at a subcellular level in three-dimensional space. Although clearing and imaging of the whole organ have been used to study tissue biology, the microenvironment in which cells evolve to adapt to biomaterial implants or allografts in the body is poorly understood. Obtaining high-resolution information from complex cell-biomaterial interactions with volumetric landscapes represents a key challenge in the fields of biomaterials and regenerative medicine. To provide a new approach to examine how tissue responds to biomaterial implants, we apply cleared tissue light-sheet microscopy and three-dimensional reconstruction to utilize the wealth of autofluorescence information for visualizing and contrasting anatomical structures. This study demonstrates the adaptability of the clearing and imaging technique to provide sub-cellular resolution (0.6 μm isotropic) 3D maps of various tissue types, using samples from fully intact peritoneal organs to volumetric muscle loss injury specimens. Specifically, in the volumetric muscle loss injury model, we provide 3D visualization of the implanted extracellular matrix biomaterial in the wound bed of the quadricep muscle groups and further apply computational-driven image classification to analyze the autofluorescence spectrum at multiple emission wavelengths to categorize tissue types at the injured site interacting with the biomaterial scaffolds.
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Affiliation(s)
- Tran B Ngo
- Section on Immunoengineering, Bioengineering and Technology Acceleration Center, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Sabrina DeStefano
- Section on Immunoengineering, Bioengineering and Technology Acceleration Center, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Jiamin Liu
- Advanced Imaging and Microscopy Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Yijun Su
- Advanced Imaging and Microscopy Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Kaitlyn Sadtler
- Section on Immunoengineering, Bioengineering and Technology Acceleration Center, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
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11
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Lauziere A, Christensen R, Shroff H, Balan R. An Exact Hypergraph Matching algorithm for posture identification in embryonic C. elegans. PLoS One 2022; 17:e0277343. [PMID: 36445888 PMCID: PMC9707761 DOI: 10.1371/journal.pone.0277343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 10/25/2022] [Indexed: 12/03/2022] Open
Abstract
The nematode Caenorhabditis elegans (C. elegans) is a model organism used frequently in developmental biology and neurobiology [White, (1986), Sulston, (1983), Chisholm, (2016) and Rapti, (2020)]. The C. elegans embryo can be used for cell tracking studies to understand how cell movement drives the development of specific embryonic tissues. Analyses in late-stage development are complicated by bouts of rapid twitching motions which invalidate traditional cell tracking approaches. However, the embryo possesses a small set of cells which may be identified, thereby defining the coiled embryo's posture [Christensen, 2015]. The posture serves as a frame of reference, facilitating cell tracking even in the presence of twitching. Posture identification is nevertheless challenging due to the complete repositioning of the embryo between sampled images. Current approaches to posture identification rely on time-consuming manual efforts by trained users which limits the efficiency of subsequent cell tracking. Here, we cast posture identification as a point-set matching task in which coordinates of seam cell nuclei are identified to jointly recover the posture. Most point-set matching methods comprise coherent point transformations that use low order objective functions [Zhou, (2016) and Zhang, (2019)]. Hypergraphs, an extension of traditional graphs, allow more intricate modeling of relationships between objects, yet existing hypergraphical point-set matching methods are limited to heuristic algorithms which do not easily scale to handle higher degree hypergraphs [Duchenne, (2010), Chertok, (2010) and Lee, (2011)]. Our algorithm, Exact Hypergraph Matching (EHGM), adapts the classical branch-and-bound paradigm to dynamically identify a globally optimal correspondence between point-sets under an arbitrarily intricate hypergraphical model. EHGM with hypergraphical models inspired by C. elegans embryo shape identified posture more accurately (56%) than established point-set matching methods (27%), correctly identifying twice as many sampled postures as a leading graphical approach. Posterior region seeding empowered EHGM to correctly identify 78% of postures while reducing runtime, demonstrating the efficacy of the method on a cutting-edge problem in developmental biology.
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Affiliation(s)
- Andrew Lauziere
- Department of Mathematics, University of Maryland, College Park, MD, United States of America
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, United States of America
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, United States of America
| | - Radu Balan
- Department of Mathematics, University of Maryland, College Park, MD, United States of America
- Center for Scientific Computation and Mathematical Modeling (CSCAMM), University of Maryland, College Park, MD, United States of America
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12
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Abstract
Fluorescence microscopy is a highly effective tool for interrogating biological structure and function, particularly when imaging across multiple spatiotemporal scales. Here we survey recent innovations and applications in the relatively understudied area of multiscale fluorescence imaging of living samples. We discuss fundamental challenges in live multiscale imaging and describe successful examples that highlight the power of this approach. We attempt to synthesize general strategies from these test cases, aiming to help accelerate progress in this exciting area.
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Affiliation(s)
- Yicong Wu
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Hari Shroff
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
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13
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Wheatley BA, Rey-Suarez I, Hourwitz MJ, Kerr S, Shroff H, Fourkas JT, Upadhyaya A. Nanotopography modulates cytoskeletal organization and dynamics during T cell activation. Mol Biol Cell 2022; 33:ar88. [PMID: 35830602 PMCID: PMC9582624 DOI: 10.1091/mbc.e21-12-0601] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Exposure to MHC-antigen complexes on the surface of antigen-presenting cells (APCs) activates T cells, inducing the formation of the immune synapse (IS). Antigen detection at the APC surface is thus a critical step in the adaptive immune response. The physical properties of antigen-presenting surfaces encountered by T cells in vivo are believed to modulate T cell activation and proliferation. Although stiffness and ligand mobility influence IS formation, the effect of the complex topography of the APC surface on this process is not well understood. Here we investigate how nanotopography modulates cytoskeletal dynamics and signaling during the early stages of T cell activation using high-resolution fluorescence microscopy on nanofabricated surfaces with parallel nanoridges of different spacings. We find that although nanoridges reduce the maximum spread area as compared with cells on flat surfaces, the ridges enhance the accumulation of actin and the signaling kinase ZAP-70 at the IS. Actin polymerization is more dynamic in the presence of ridges, which influence the directionality of both actin flows and microtubule (MT) growth. Our results demonstrate that the topography of the activating surface exerts both global effects on T cell morphology and local changes in actin and MT dynamics, collectively influencing T cell signaling.
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Affiliation(s)
- Brittany A Wheatley
- Department of Integrative Structural and Computational Biology and.,Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33458
| | - Ivan Rey-Suarez
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742
| | - Matt J Hourwitz
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Sarah Kerr
- Department of Physics, University of Colorado, Boulder, CO 80302
| | - Hari Shroff
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - John T Fourkas
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742.,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742.,Maryland Quantum Materials Center, University of Maryland, College Park, MD 20742
| | - Arpita Upadhyaya
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742.,Department of Physics, University of Maryland, College Park, MD 20742
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14
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Ardiel EL, Lauziere A, Xu S, Harvey BJ, Christensen RP, Nurrish S, Kaplan JM, Shroff H. Stereotyped behavioral maturation and rhythmic quiescence in C.elegans embryos. eLife 2022; 11:76836. [PMID: 35929725 PMCID: PMC9448323 DOI: 10.7554/elife.76836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 08/01/2022] [Indexed: 11/18/2022] Open
Abstract
Systematic analysis of rich behavioral recordings is being used to uncover how circuits encode complex behaviors. Here, we apply this approach to embryos. What are the first embryonic behaviors and how do they evolve as early neurodevelopment ensues? To address these questions, we present a systematic description of behavioral maturation for Caenorhabditis elegans embryos. Posture libraries were built using a genetically encoded motion capture suit imaged with light-sheet microscopy and annotated using custom tracking software. Analysis of cell trajectories, postures, and behavioral motifs revealed a stereotyped developmental progression. Early movement is dominated by flipping between dorsal and ventral coiling, which gradually slows into a period of reduced motility. Late-stage embryos exhibit sinusoidal waves of dorsoventral bends, prolonged bouts of directed motion, and a rhythmic pattern of pausing, which we designate slow wave twitch (SWT). Synaptic transmission is required for late-stage motion but not for early flipping nor the intervening inactive phase. A high-throughput behavioral assay and calcium imaging revealed that SWT is elicited by the rhythmic activity of a quiescence-promoting neuron (RIS). Similar periodic quiescent states are seen prenatally in diverse animals and may play an important role in promoting normal developmental outcomes.
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Affiliation(s)
- Evan L Ardiel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Andrew Lauziere
- National Institute of Biomedical Imaging and Bioengineering, Bethesda, United States
| | - Stephen Xu
- National Institute of Biomedical Imaging and Bioengineering, Bethesda, United States
| | - Brandon J Harvey
- National Institute of Biomedical Imaging and Bioengineering, Bethesda, United States
| | | | - Stephen Nurrish
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Joshua M Kaplan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Hari Shroff
- National Institute of Biomedical Imaging and Bioengineering, Bethesda, United States
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15
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Zhao H, Nguyen A, Wu D, Li Y, Hassan SA, Chen J, Shroff H, Piszczek G, Schuck P. Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. PNAS Nexus 2022; 1:pgac049. [PMID: 35783502 PMCID: PMC9235412 DOI: 10.1093/pnasnexus/pgac049] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/19/2022] [Indexed: 02/06/2023]
Abstract
Worldwide SARS-CoV-2 sequencing efforts track emerging mutations in its spike protein, as well as characteristic mutations in other viral proteins. Besides their epidemiological importance, the observed SARS-CoV-2 sequences present an ensemble of viable protein variants, and thereby a source of information on viral protein structure and function. Charting the mutational landscape of the nucleocapsid (N) protein that facilitates viral assembly, we observe variability exceeding that of the spike protein, with more than 86% of residues that can be substituted, on average by three to four different amino acids. However, mutations exhibit an uneven distribution that tracks known structural features but also reveals highly protected stretches of unknown function. One of these conserved regions is in the central disordered linker proximal to the N-G215C mutation that has become dominant in the Delta variant, outcompeting G215 variants without further spike or N-protein substitutions. Structural models suggest that the G215C mutation stabilizes conserved transient helices in the disordered linker serving as protein-protein interaction interfaces. Comparing Delta variant N-protein to its ancestral version in biophysical experiments, we find a significantly more compact and less disordered structure. N-G215C exhibits substantially stronger self-association, shifting the unliganded protein from a dimeric to a tetrameric oligomeric state, which leads to enhanced coassembly with nucleic acids. This suggests that the sequence variability of N-protein is mirrored by high plasticity of N-protein biophysical properties, which we hypothesize can be exploited by SARS-CoV-2 to achieve greater efficiency of viral assembly, and thereby enhanced infectivity.
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Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergio A Hassan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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16
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Patel A, Wu Y, Han X, Su Y, Maugel T, Shroff H, Roy S. Cytonemes coordinate asymmetric signaling and organization in the Drosophila muscle progenitor niche. Nat Commun 2022; 13:1185. [PMID: 35246530 PMCID: PMC8897416 DOI: 10.1038/s41467-022-28587-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/02/2022] [Indexed: 12/29/2022] Open
Abstract
Asymmetric signaling and organization in the stem-cell niche determine stem-cell fates. Here, we investigate the basis of asymmetric signaling and stem-cell organization using the Drosophila wing-disc that creates an adult muscle progenitor (AMP) niche. We show that AMPs extend polarized cytonemes to contact the disc epithelial junctions and adhere themselves to the disc/niche. Niche-adhering cytonemes localize FGF-receptor to selectively adhere to the FGF-producing disc and receive FGFs in a contact-dependent manner. Activation of FGF signaling in AMPs, in turn, reinforces disc-specific cytoneme polarity/adhesion, which maintains their disc-proximal positions. Loss of cytoneme-mediated adhesion promotes AMPs to lose niche occupancy and FGF signaling, occupy a disc-distal position, and acquire morphological hallmarks of differentiation. Niche-specific AMP organization and diversification patterns are determined by localized expression and presentation patterns of two different FGFs in the wing-disc and their polarized target-specific distribution through niche-adhering cytonemes. Thus, cytonemes are essential for asymmetric signaling and niche-specific AMP organization.
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Affiliation(s)
- Akshay Patel
- grid.164295.d0000 0001 0941 7177Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD USA
| | - Yicong Wu
- grid.94365.3d0000 0001 2297 5165Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD USA
| | - Xiaofei Han
- grid.94365.3d0000 0001 2297 5165Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD USA
| | - Yijun Su
- grid.94365.3d0000 0001 2297 5165Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD USA ,grid.94365.3d0000 0001 2297 5165Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD USA
| | - Tim Maugel
- grid.164295.d0000 0001 0941 7177Department of Biology, Laboratory for Biological Ultrastructure, University of Maryland, College Park, MD USA
| | - Hari Shroff
- grid.94365.3d0000 0001 2297 5165Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD USA ,grid.94365.3d0000 0001 2297 5165Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD USA
| | - Sougata Roy
- grid.164295.d0000 0001 0941 7177Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD USA
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17
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Zhao H, Nguyen A, Wu D, Li Y, Hassan SA, Chen J, Shroff H, Piszczek G, Schuck P. Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. bioRxiv 2022:2022.02.08.479556. [PMID: 35169797 PMCID: PMC8845419 DOI: 10.1101/2022.02.08.479556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Worldwide SARS-CoV-2 sequencing efforts track emerging mutations in its spike protein, as well as characteristic mutations in other viral proteins. Besides their epidemiological importance, the observed SARS-CoV-2 sequences present an ensemble of viable protein variants, and thereby a source of information on viral protein structure and function. Charting the mutational landscape of the nucleocapsid (N) protein that facilitates viral assembly, we observe variability exceeding that of the spike protein, with more than 86% of residues that can be substituted, on average by 3-4 different amino acids. However, mutations exhibit an uneven distribution that tracks known structural features but also reveals highly protected stretches of unknown function. One of these conserved regions is in the central disordered linker proximal to the N-G215C mutation that has become dominant in the Delta variant, outcompeting G215 variants without further spike or N-protein substitutions. Structural models suggest that the G215C mutation stabilizes conserved transient helices in the disordered linker serving as protein-protein interaction interfaces. Comparing Delta variant N-protein to its ancestral version in biophysical experiments, we find a significantly more compact and less disordered structure. N-G215C exhibits substantially stronger self-association, shifting the unliganded protein from a dimeric to a tetrameric oligomeric state, which leads to enhanced co-assembly with nucleic acids. This suggests that the sequence variability of N-protein is mirrored by high plasticity of N-protein biophysical properties, which we hypothesize can be exploited by SARS-CoV-2 to achieve greater efficiency of viral assembly, and thereby enhanced infectivity.
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Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergio A. Hassan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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18
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Wu Y, Han X, Su Y, Glidewell M, Daniels JS, Liu J, Sengupta T, Rey-Suarez I, Fischer R, Patel A, Combs C, Sun J, Wu X, Christensen R, Smith C, Bao L, Sun Y, Duncan LH, Chen J, Pommier Y, Shi YB, Murphy E, Roy S, Upadhyaya A, Colón-Ramos D, La Riviere P, Shroff H. Multiview confocal super-resolution microscopy. Nature 2021; 600:279-284. [PMID: 34837071 PMCID: PMC8686173 DOI: 10.1038/s41586-021-04110-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/07/2021] [Indexed: 12/31/2022]
Abstract
Confocal microscopy1 remains a major workhorse in biomedical optical microscopy owing to its reliability and flexibility in imaging various samples, but suffers from substantial point spread function anisotropy, diffraction-limited resolution, depth-dependent degradation in scattering samples and volumetric bleaching2. Here we address these problems, enhancing confocal microscopy performance from the sub-micrometre to millimetre spatial scale and the millisecond to hour temporal scale, improving both lateral and axial resolution more than twofold while simultaneously reducing phototoxicity. We achieve these gains using an integrated, four-pronged approach: (1) developing compact line scanners that enable sensitive, rapid, diffraction-limited imaging over large areas; (2) combining line-scanning with multiview imaging, developing reconstruction algorithms that improve resolution isotropy and recover signal otherwise lost to scattering; (3) adapting techniques from structured illumination microscopy, achieving super-resolution imaging in densely labelled, thick samples; (4) synergizing deep learning with these advances, further improving imaging speed, resolution and duration. We demonstrate these capabilities on more than 20 distinct fixed and live samples, including protein distributions in single cells; nuclei and developing neurons in Caenorhabditis elegans embryos, larvae and adults; myoblasts in imaginal disks of Drosophila wings; and mouse renal, oesophageal, cardiac and brain tissues.
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Affiliation(s)
- Yicong Wu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
| | - Xiaofei Han
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Department of Automation, Tsinghua University, Beijing, China
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Leica Microsystems, Buffalo Grove, IL, USA
- SVision, Bellevue, WA, USA
| | | | | | - Jiamin Liu
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Titas Sengupta
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Ivan Rey-Suarez
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Robert Fischer
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Akshay Patel
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Christian Combs
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, MD, USA
| | - Junhui Sun
- Laboratory of Cardiac Physiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xufeng Wu
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, MD, USA
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Corey Smith
- Department of Radiology, University of Chicago, Chicago, IL, USA
| | - Lingyu Bao
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yilun Sun
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Leighton H Duncan
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Elizabeth Murphy
- Laboratory of Cardiac Physiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sougata Roy
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Arpita Upadhyaya
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
| | - Daniel Colón-Ramos
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
- Instituto de Neurobiología, Recinto de Ciencias Médicas, Universidad de Puerto Rico, San Juan, Puerto Rico
| | - Patrick La Riviere
- Department of Radiology, University of Chicago, Chicago, IL, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
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19
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Sengupta T, Koonce NL, Vázquez-Martínez N, Moyle MW, Duncan LH, Emerson SE, Han X, Shao L, Wu Y, Santella A, Fan L, Bao Z, Mohler W, Shroff H, Colón-Ramos DA. Differential adhesion regulates neurite placement via a retrograde zippering mechanism. eLife 2021; 10:71171. [PMID: 34783657 PMCID: PMC8843091 DOI: 10.7554/elife.71171] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
During development, neurites and synapses segregate into specific neighborhoods or layers within nerve bundles. The developmental programs guiding placement of neurites in specific layers, and hence their incorporation into specific circuits, are not well understood. We implement novel imaging methods and quantitative models to document the embryonic development of the C. elegans brain neuropil, and discover that differential adhesion mechanisms control precise placement of single neurites onto specific layers. Differential adhesion is orchestrated via developmentally-regulated expression of the IgCAM SYG-1, and its partner ligand SYG-2. Changes in SYG-1 expression across neuropil layers result in changes in adhesive forces, which sort SYG-2-expressing neurons. Sorting to layers occurs, not via outgrowth from the neurite tip, but via an alternate mechanism of retrograde zippering, involving interactions between neurite shafts. Our study indicates that biophysical principles from differential adhesion govern neurite placement and synaptic specificity in vivo in developing neuropil bundles.
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Affiliation(s)
- Titas Sengupta
- Yale University School of Medicine, New Haven, United States
| | - Noelle L Koonce
- Yale University School of Medicine, New Haven, United States
| | | | - Mark W Moyle
- Yale University School of Medicine, New Haven, United States
| | | | - Sarah E Emerson
- Yale University School of Medicine, New Haven, United States
| | - Xiaofei Han
- National Institutes of Health, Bethesda, United States
| | - Lin Shao
- Yale University School of Medicine, New Haven, United States
| | - Yicong Wu
- National Institutes of Health, Bethesda, United States
| | - Anthony Santella
- Developmental Biology Program, Molecular Cytology Core, Sloan-Kettering Institute, New York, United States
| | - Li Fan
- Helen and Robert Appel Alzheimer's Disease Institute, Weill Cornell Medicine, New York, United States
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, United States
| | - William Mohler
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States
| | - Hari Shroff
- National Institutes of Health, Bethesda, United States
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20
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Elliott AD, Berndt A, Houpert M, Roy S, Scott RL, Chow CC, Shroff H, White BH. Pupal behavior emerges from unstructured muscle activity in response to neuromodulation in Drosophila. eLife 2021; 10:68656. [PMID: 34236312 PMCID: PMC8331185 DOI: 10.7554/elife.68656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Identifying neural substrates of behavior requires defining actions in terms that map onto brain activity. Brain and muscle activity naturally correlate via the output of motor neurons, but apart from simple movements it has been difficult to define behavior in terms of muscle contractions. By mapping the musculature of the pupal fruit fly and comprehensively imaging muscle activation at single-cell resolution, we here describe a multiphasic behavioral sequence in Drosophila. Our characterization identifies a previously undescribed behavioral phase and permits extraction of major movements by a convolutional neural network. We deconstruct movements into a syllabary of co-active muscles and identify specific syllables that are sensitive to neuromodulatory manipulations. We find that muscle activity shows considerable variability, with sequential increases in stereotypy dependent upon neuromodulation. Our work provides a platform for studying whole-animal behavior, quantifying its variability across multiple spatiotemporal scales, and analyzing its neuromodulatory regulation at cellular resolution. How do we find out how the brain works? One way is to use imaging techniques to visualise an animal’s brain in action as it performs simple behaviours: as the animal moves, parts of its brain light up under the microscope. For laboratory animals like fruit flies, which have relatively small brains, this lets us observe their brain activity right down to the level of individual brain cells. The brain directs movements via collective activity of the body’s muscles. Our ability to track the activity of individual muscles is, however, more limited than our ability to observe single brain cells: even modern imaging technology still cannot monitor the activity of all the muscle cells in an animal’s body as it moves about. Yet this is precisely the information that scientists need to fully understand how the brain generates behaviour. Fruit flies perform specific behaviours at certain stages of their life cycle. When the fly pupa begins to metamorphose into an adult insect, it performs a fixed sequence of movements involving a set number of muscles, which is called the pupal ecdysis sequence. This initial movement sequence and the rest of metamorphosis both occur within the confines of the pupal case, which is a small, hardened shell surrounding the whole animal. Elliott et al. set out to determine if the fruit fly pupa’s ecdysis sequence could be used as a kind of model, to describe a simple behaviour at the level of individual muscles. Imaging experiments used fly pupae that were genetically engineered to produce an activity-dependent fluorescent protein in their muscle cells. Pupal cases were treated with a chemical to make them transparent, allowing easy observation of their visually ‘labelled’ muscles. This yielded a near-complete record of muscle activity during metamorphosis. Initially, individual muscles became active in small groups. The groups then synchronised with each other over the different regions of the pupa’s body to form distinct movements, much as syllables join to form words. This synchronisation was key to progression through metamorphosis and was co-ordinated at each step by specialised nerve cells that produce or respond to specific hormones. These results reveal how the brain might direct muscle activity to produce movement patterns. In the future, Elliott et al. hope to compare data on muscle activity with comprehensive records of brain cell activity, to shed new light on how the brain, muscles, and other factors work together to control behaviour.
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Affiliation(s)
- Amicia D Elliott
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States.,National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Adama Berndt
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States
| | - Matthew Houpert
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States
| | - Snehashis Roy
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States
| | - Robert L Scott
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States
| | - Carson C Chow
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Hari Shroff
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Benjamin H White
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States
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21
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Miyoshi T, Belyantseva IA, Kitajiri SI, Miyajima H, Nishio SY, Usami SI, Kim BJ, Choi BY, Omori K, Shroff H, Friedman TB. Human deafness-associated variants alter the dynamics of key molecules in hair cell stereocilia F-actin cores. Hum Genet 2021; 141:363-382. [PMID: 34232383 DOI: 10.1007/s00439-021-02304-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/15/2021] [Indexed: 12/16/2022]
Abstract
Stereocilia protrude up to 100 µm from the apical surface of vertebrate inner ear hair cells and are packed with cross-linked filamentous actin (F-actin). They function as mechanical switches to convert sound vibration into electrochemical neuronal signals transmitted to the brain. Several genes encode molecular components of stereocilia including actin monomers, actin regulatory and bundling proteins, motor proteins and the proteins of the mechanotransduction complex. A stereocilium F-actin core is a dynamic system, which is continuously being remodeled while maintaining an outwardly stable architecture under the regulation of F-actin barbed-end cappers, severing proteins and crosslinkers. The F-actin cores of stereocilia also provide a pathway for motor proteins to transport cargos including components of tip-link densities, scaffolding proteins and actin regulatory proteins. Deficiencies and mutations of stereocilia components that disturb this "dynamic equilibrium" in stereocilia can induce morphological changes and disrupt mechanotransduction causing sensorineural hearing loss, best studied in mouse and zebrafish models. Currently, at least 23 genes, associated with human syndromic and nonsyndromic hearing loss, encode proteins involved in the development and maintenance of stereocilia F-actin cores. However, it is challenging to predict how variants associated with sensorineural hearing loss segregating in families affect protein function. Here, we review the functions of several molecular components of stereocilia F-actin cores and provide new data from our experimental approach to directly evaluate the pathogenicity and functional impact of reported and novel variants of DIAPH1 in autosomal-dominant DFNA1 hearing loss using single-molecule fluorescence microscopy.
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Affiliation(s)
- Takushi Miyoshi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD, 20892, USA. .,Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD, 20892, USA
| | - Shin-Ichiro Kitajiri
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 390-8621, Matsumoto, Japan
| | - Hiroki Miyajima
- Department of Otolaryngology, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan.,Department of Otolaryngology, Aizawa Hospital, Matsumoto, 390-8510, Japan
| | - Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 390-8621, Matsumoto, Japan
| | - Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 390-8621, Matsumoto, Japan
| | - Bong Jik Kim
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University College of Medicine, Chungnam National University Sejong Hospital, Sejong, 30099, South Korea.,Brain Research Institute, Chungnam National University College of Medicine, Daejeon, 35015, South Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, 13620, South Korea
| | - Koichi Omori
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD, 20892, USA
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22
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Campanello L, Traver MK, Shroff H, Schaefer BC, Losert W. Signaling through polymerization and degradation: Analysis and simulations of T cell activation mediated by Bcl10. PLoS Comput Biol 2021; 17:e1007986. [PMID: 34014917 PMCID: PMC8184007 DOI: 10.1371/journal.pcbi.1007986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/07/2021] [Accepted: 04/28/2021] [Indexed: 12/05/2022] Open
Abstract
The adaptive immune system serves as a potent and highly specific defense mechanism against pathogen infection. One component of this system, the effector T cell, facilitates pathogen clearance upon detection of specific antigens by the T cell receptor (TCR). A critical process in effector T cell activation is transmission of signals from the TCR to a key transcriptional regulator, NF-κB. The transmission of this signal involves a highly dynamic process in which helical filaments of Bcl10, a key protein constituent of the TCR signaling cascade, undergo competing processes of polymeric assembly and macroautophagy-dependent degradation. Through computational analysis of three-dimensional, super-resolution optical micrographs, we quantitatively characterize TCR-stimulated Bcl10 filament assembly and length dynamics, and demonstrate that filaments become shorter over time. Additionally, we develop an image-based, bootstrap-like resampling method that demonstrates the preferred association between autophagosomes and both Bcl10-filament ends and punctate-Bcl10 structures, implying that autophagosome-driven macroautophagy is directly responsible for Bcl10 filament shortening. We probe Bcl10 polymerization-depolymerization dynamics with a stochastic Monte-Carlo simulation of nucleation-limited filament assembly and degradation, and we show that high probabilities of filament nucleation in response to TCR engagement could provide the observed robust, homogeneous, and tunable response dynamic. Furthermore, we demonstrate that the speed of filament disassembly preferentially at filament ends provides effective regulatory control. Taken together, these data suggest that Bcl10 filament growth and degradation act as an excitable system that provides a digital response mechanism and the reliable timing critical for T cell activation and regulatory processes. The immune system serves to protect organisms against pathogen-mediated disease. While a strong immune response is needed to eliminate pathogens in host organisms, immune responses that are too robust or too persistent can trigger autoimmune disorders, cancer, and a variety of additional serious human pathologies. Thus, a careful balance of activating and inhibitory mechanisms is necessary to prevent detrimental health outcomes of immune responses. For example, activated effector T cells marshal the immune response and direct killing of pathogen-infected cells; however, effector T cells that are chronically activated can damage and destroy healthy tissue. Here, we study an important internal activation pathway in effector T cells that involves the growth and counterbalancing disassembly (involving a process called macroautophagy) of filamentous cytoplasmic signaling structures. We utilize image analysis of 3-D super-resolution images and Monte Carlo simulations to study a key signal-transduction protein, Bcl10. We found that the speed of filament disassembly has the greatest effect on the magnitude and duration of the response, implying that pharmaceutical interventions aimed at macroautophagy may have substantial impact on effector T cell function. Given that filamentous structures are utilized in numerous immune signaling pathways, our analysis methods could have broad applicability in the signal transduction field.
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Affiliation(s)
- Leonard Campanello
- Department of Physics, University of Maryland College Park, College Park, Maryland, United States of America
- Institute for Physical Science and Technology, University of Maryland College Park, College Park, Maryland, United States of America
| | - Maria K. Traver
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Hari Shroff
- Department of Physics, University of Maryland College Park, College Park, Maryland, United States of America
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brian C. Schaefer
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- * E-mail: (BCS); (WL)
| | - Wolfgang Losert
- Department of Physics, University of Maryland College Park, College Park, Maryland, United States of America
- Institute for Physical Science and Technology, University of Maryland College Park, College Park, Maryland, United States of America
- * E-mail: (BCS); (WL)
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23
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Han X, Su Y, White H, O'Neill KM, Morgan NY, Christensen R, Potarazu D, Vishwasrao HD, Xu S, Sun Y, Huang SY, Moyle MW, Dai Q, Pommier Y, Giniger E, Albrecht DR, Probst R, Shroff H. A polymer index-matched to water enables diverse applications in fluorescence microscopy. Lab Chip 2021; 21:1549-1562. [PMID: 33629685 PMCID: PMC8058278 DOI: 10.1039/d0lc01233e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We demonstrate diffraction-limited and super-resolution imaging through thick layers (tens-hundreds of microns) of BIO-133, a biocompatible, UV-curable, commercially available polymer with a refractive index (RI) matched to water. We show that cells can be directly grown on BIO-133 substrates without the need for surface passivation and use this capability to perform extended time-lapse volumetric imaging of cellular dynamics 1) at isotropic resolution using dual-view light-sheet microscopy, and 2) at super-resolution using instant structured illumination microscopy. BIO-133 also enables immobilization of 1) Drosophila tissue, allowing us to track membrane puncta in pioneer neurons, and 2) Caenorhabditis elegans, which allows us to image and inspect fine neural structure and to track pan-neuronal calcium activity over hundreds of volumes. Finally, BIO-133 is compatible with other microfluidic materials, enabling optical and chemical perturbation of immobilized samples, as we demonstrate by performing drug and optogenetic stimulation on cells and C. elegans.
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Affiliation(s)
- Xiaofei Han
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hamilton White
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA. and Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Kate M O'Neill
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA and Institute for Physical Science and Technology, University of Maryland College Park, College Park, MD 20742, USA
| | - Nicole Y Morgan
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Deepika Potarazu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen Xu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shar-Yin Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark W Moyle
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dirk R Albrecht
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA. and Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Roland Probst
- ACUITYnano, Innovation in Biomedical Imaging, North Bethesda, MD 20850, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA and Marine Biological Laboratory Fellows Program, Woods Hole, MA 02543, USA
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24
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Rey-Suarez I, Rogers N, Kerr S, Shroff H, Upadhyaya A. Actomyosin dynamics modulate microtubule deformation and growth during T-cell activation. Mol Biol Cell 2021; 32:1641-1653. [PMID: 33826369 PMCID: PMC8684730 DOI: 10.1091/mbc.e20-10-0685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Activation of T-cells leads to the formation of immune synapses (ISs) with antigen-presenting cells. This requires T-cell polarization and coordination between the actomyosin and microtubule cytoskeletons. The interactions between these two cytoskeletal components during T-cell activation are not well understood. Here, we elucidate the interactions between microtubules and actin at the IS with high-resolution fluorescence microscopy. We show that microtubule growth dynamics in the peripheral actin-rich region is distinct from that in the central actin-free region. We further demonstrate that these differences arise from differential involvement of Arp2/3- and formin-nucleated actin structures. Formin inhibition results in a moderate decrease in microtubule growth rates, which is amplified in the presence of integrin engagement. In contrast, Arp2/3 inhibition leads to an increase in microtubule growth rates. We find that microtubule filaments are more deformed and exhibit greater shape fluctuations in the periphery of the IS than at the center. Using small molecule inhibitors, we show that actin dynamics and actomyosin contractility play key roles in defining microtubule deformations and shape fluctuations. Our results indicate a mechanical coupling between the actomyosin and microtubule systems during T-cell activation, whereby different actin structures influence microtubule dynamics in distinct ways.
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Affiliation(s)
- Ivan Rey-Suarez
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742
| | - Nate Rogers
- Department of Physics, University of Maryland, College Park, MD 20742
| | - Sarah Kerr
- Department of Physics, University of Colorado, Boulder, CO 80302
| | - Hari Shroff
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Arpita Upadhyaya
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742.,Department of Physics, University of Maryland, College Park, MD 20742
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25
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Curd A, Leng J, Hughes RE, Cleasby AJ, Rogers B, Trinh CH, Baird MA, Takagi Y, Tiede C, Sieben C, Manley S, Schlichthaerle T, Jungmann R, Ries J, Shroff H, Peckham M. Nanoscale Pattern Extraction from Relative Positions of Sparse 3D Localizations. Nano Lett 2021; 21:1213-1220. [PMID: 33253583 PMCID: PMC7883386 DOI: 10.1021/acs.nanolett.0c03332] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/24/2020] [Indexed: 05/23/2023]
Abstract
Inferring the organization of fluorescently labeled nanosized structures from single molecule localization microscopy (SMLM) data, typically obscured by stochastic noise and background, remains challenging. To overcome this, we developed a method to extract high-resolution ordered features from SMLM data that requires only a low fraction of targets to be localized with high precision. First, experimentally measured localizations are analyzed to produce relative position distributions (RPDs). Next, model RPDs are constructed using hypotheses of how the molecule is organized. Finally, a statistical comparison is used to select the most likely model. This approach allows pattern recognition at sub-1% detection efficiencies for target molecules, in large and heterogeneous samples and in 2D and 3D data sets. As a proof-of-concept, we infer ultrastructure of Nup107 within the nuclear pore, DNA origami structures, and α-actinin-2 within the cardiomyocyte Z-disc and assess the quality of images of centrioles to improve the averaged single-particle reconstruction.
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Affiliation(s)
- Alistair
P. Curd
- School
of Molecular and Cellular Biology, University
of Leeds, Leeds LS2 9JT, United Kingdom
| | - Joanna Leng
- School
of Computing, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Ruth E. Hughes
- School
of Molecular and Cellular Biology, University
of Leeds, Leeds LS2 9JT, United Kingdom
| | - Alexa J. Cleasby
- School
of Molecular and Cellular Biology, University
of Leeds, Leeds LS2 9JT, United Kingdom
| | - Brendan Rogers
- School
of Molecular and Cellular Biology, University
of Leeds, Leeds LS2 9JT, United Kingdom
| | - Chi H. Trinh
- School
of Molecular and Cellular Biology, University
of Leeds, Leeds LS2 9JT, United Kingdom
| | - Michelle A. Baird
- Cell
and Developmental Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yasuharu Takagi
- Cell
and Developmental Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christian Tiede
- School
of Molecular and Cellular Biology, University
of Leeds, Leeds LS2 9JT, United Kingdom
| | - Christian Sieben
- Laboratory
of Experimental Biophysics, École
Polytechnique Fédérale de Lausanne, BSP 427 (Cubotron UNIL), Rte de
la Sorge, CH-1015 Lausanne, Switzerland
| | - Suliana Manley
- Laboratory
of Experimental Biophysics, École
Polytechnique Fédérale de Lausanne, BSP 427 (Cubotron UNIL), Rte de
la Sorge, CH-1015 Lausanne, Switzerland
| | - Thomas Schlichthaerle
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Munich, Germany
- Faculty
of Physics and Center for Nanoscience, LMU
Munich, 80539 Munich, Germany
| | - Ralf Jungmann
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Munich, Germany
- Faculty
of Physics and Center for Nanoscience, LMU
Munich, 80539 Munich, Germany
| | - Jonas Ries
- Cell Biology
and Biophysics Unit, European Molecular
Biology Laboratory, 69117 Heidelberg, Germany
| | - Hari Shroff
- Laboratory
of High Resolution Optical Imaging, National Institute of Biomedical
Imaging and Bioengineering, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Michelle Peckham
- School
of Molecular and Cellular Biology, University
of Leeds, Leeds LS2 9JT, United Kingdom
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26
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Miyoshi T, Zhang Q, Miyake T, Watanabe S, Ohnishi H, Chen J, Vishwasrao HD, Chakraborty O, Belyantseva IA, Perrin BJ, Shroff H, Friedman TB, Omori K, Watanabe N. Semi-automated single-molecule microscopy screening of fast-dissociating specific antibodies directly from hybridoma cultures. Cell Rep 2021; 34:108708. [PMID: 33535030 PMCID: PMC7904085 DOI: 10.1016/j.celrep.2021.108708] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/16/2020] [Accepted: 01/08/2021] [Indexed: 11/18/2022] Open
Abstract
Fast-dissociating, specific antibodies are single-molecule imaging probes that transiently interact with their targets and are used in biological applications including image reconstruction by integrating exchangeable single-molecule localization (IRIS), a multiplexable super-resolution microscopy technique. Here, we introduce a semi-automated screen based on single-molecule total internal reflection fluorescence (TIRF) microscopy of antibody-antigen binding, which allows for identification of fast-dissociating monoclonal antibodies directly from thousands of hybridoma cultures. We develop monoclonal antibodies against three epitope tags (FLAG-tag, S-tag, and V5-tag) and two F-actin crosslinking proteins (plastin and espin). Specific antibodies show fast dissociation with half-lives ranging from 0.98 to 2.2 s. Unexpectedly, fast-dissociating yet specific antibodies are not so rare. A combination of fluorescently labeled Fab probes synthesized from these antibodies and light-sheet microscopy, such as dual-view inverted selective plane illumination microscopy (diSPIM), reveal rapid turnover of espin within long-lived F-actin cores of inner-ear sensory hair cell stereocilia, demonstrating that fast-dissociating specific antibodies can identify novel biological phenomena.
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Affiliation(s)
- Takushi Miyoshi
- Laboratory of Single-Molecule Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Department of Otolaryngology - Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Qianli Zhang
- Laboratory of Single-Molecule Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Takafumi Miyake
- Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Shin Watanabe
- Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroe Ohnishi
- Department of Otolaryngology - Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Oisorjo Chakraborty
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benjamin J Perrin
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA; Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Koichi Omori
- Department of Otolaryngology - Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Naoki Watanabe
- Laboratory of Single-Molecule Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.
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27
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Dalle Nogare DE, Natesh N, Vishwasrao HD, Shroff H, Chitnis AB. Zebrafish Posterior Lateral Line primordium migration requires interactions between a superficial sheath of motile cells and the skin. eLife 2020; 9:58251. [PMID: 33237853 PMCID: PMC7688310 DOI: 10.7554/elife.58251] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
The Zebrafish Posterior Lateral Line primordium migrates in a channel between the skin and somites. Its migration depends on the coordinated movement of its mesenchymal-like leading cells and trailing cells, which form epithelial rosettes, or protoneuromasts. We describe a superficial population of flat primordium cells that wrap around deeper epithelialized cells and extend polarized lamellipodia to migrate apposed to the overlying skin. Polarization of lamellipodia extended by both superficial and deeper protoneuromast-forming cells depends on Fgf signaling. Removal of the overlying skin has similar effects on superficial and deep cells: lamellipodia are lost, blebs appear instead, and collective migration fails. When skinned embryos are embedded in Matrigel, basal and superficial lamellipodia are recovered; however, only the directionality of basal protrusions is recovered, and migration is not rescued. These observations support a key role played by superficial primordium cells and the skin in directed migration of the Posterior Lateral Line primordium.
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Affiliation(s)
- Damian E Dalle Nogare
- Section on Neural Developmental Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Naveen Natesh
- Section on Neural Developmental Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, United States
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, United States.,Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Ajay B Chitnis
- Section on Neural Developmental Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
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28
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Guo M, Li Y, Su Y, Lambert T, Nogare DD, Moyle MW, Duncan LH, Ikegami R, Santella A, Rey-Suarez I, Green D, Beiriger A, Chen J, Vishwasrao H, Ganesan S, Prince V, Waters JC, Annunziata CM, Hafner M, Mohler WA, Chitnis AB, Upadhyaya A, Usdin TB, Bao Z, Colón-Ramos D, La Riviere P, Liu H, Wu Y, Shroff H. Rapid image deconvolution and multiview fusion for optical microscopy. Nat Biotechnol 2020; 38:1337-1346. [PMID: 32601431 PMCID: PMC7642198 DOI: 10.1038/s41587-020-0560-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 05/15/2020] [Indexed: 12/11/2022]
Abstract
The contrast and resolution of images obtained with optical microscopes can be improved by deconvolution and computational fusion of multiple views of the same sample, but these methods are computationally expensive for large datasets. Here we describe theoretical and practical advances in algorithm and software design that result in image processing times that are tenfold to several thousand fold faster than with previous methods. First, we show that an 'unmatched back projector' accelerates deconvolution relative to the classic Richardson-Lucy algorithm by at least tenfold. Second, three-dimensional image-based registration with a graphics processing unit enhances processing speed 10- to 100-fold over CPU processing. Third, deep learning can provide further acceleration, particularly for deconvolution with spatially varying point spread functions. We illustrate our methods from the subcellular to millimeter spatial scale on diverse samples, including single cells, embryos and cleared tissue. Finally, we show performance enhancement on recently developed microscopes that have improved spatial resolution, including dual-view cleared-tissue light-sheet microscopes and reflective lattice light-sheet microscopes.
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Affiliation(s)
- Min Guo
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Yue Li
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Yijun Su
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Talley Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Damian Dalle Nogare
- Section on Neural Developmental Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Mark W Moyle
- Departments of Neuroscience and Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Leighton H Duncan
- Departments of Neuroscience and Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Richard Ikegami
- Departments of Neuroscience and Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony Santella
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Ivan Rey-Suarez
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Biophysics Program, University of Maryland, College Park, MD, USA
| | - Daniel Green
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Anastasia Beiriger
- Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Harshad Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Victoria Prince
- Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| | | | - Christina M Annunziata
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - William A Mohler
- Department of Genetics and Genome Sciences and Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT, USA
| | - Ajay B Chitnis
- Section on Neural Developmental Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Arpita Upadhyaya
- Biophysics Program, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Ted B Usdin
- Section on Fundamental Neuroscience, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Daniel Colón-Ramos
- Departments of Neuroscience and Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Marine Biological Laboratory Fellows Program, Woods Hole, MA, USA
- Instituto de Neurobiología, Recinto de Ciencias Médicas, Universidad de Puerto Rico, San Juan, Puerto Rico
| | - Patrick La Riviere
- Marine Biological Laboratory Fellows Program, Woods Hole, MA, USA
- Department of Radiology, University of Chicago, Chicago, IL, USA
| | - Huafeng Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.
| | - Yicong Wu
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
| | - Hari Shroff
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Marine Biological Laboratory Fellows Program, Woods Hole, MA, USA
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29
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Chandler T, Shroff H, Oldenbourg R, La Rivière P. Spatio-angular fluorescence microscopy III. Constrained angular diffusion, polarized excitation, and high-NA imaging. J Opt Soc Am A Opt Image Sci Vis 2020; 37:1465-1479. [PMID: 32902437 PMCID: PMC7931634 DOI: 10.1364/josaa.389217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We investigate rotational diffusion of fluorescent molecules in angular potential wells, the excitation and subsequent emissions from these diffusing molecules, and the imaging of these emissions with high-NA aplanatic optical microscopes. Although dipole emissions only transmit six low-frequency angular components, we show that angular structured illumination can alias higher-frequency angular components into the passband of the imaging system. We show that the number of measurable angular components is limited by the relationships between three time scales: the rotational diffusion time, the fluorescence decay time, and the acquisition time. We demonstrate our model by simulating a numerical phantom in the limits of fast angular diffusion, slow angular diffusion, and weak potentials.
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Affiliation(s)
- Talon Chandler
- University of Chicago, Department of Radiology, Chicago, Illinois 60637, USA
- Corresponding author:
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, USA
- Marine Biological Laboratory, Bell Center, Woods Hole, Massachusetts 02543, USA
| | - Rudolf Oldenbourg
- Marine Biological Laboratory, Bell Center, Woods Hole, Massachusetts 02543, USA
| | - Patrick La Rivière
- University of Chicago, Department of Radiology, Chicago, Illinois 60637, USA
- Marine Biological Laboratory, Bell Center, Woods Hole, Massachusetts 02543, USA
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30
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Trcek T, Douglas TE, Grosch M, Yin Y, Eagle WVI, Gavis ER, Shroff H, Rothenberg E, Lehmann R. Sequence-Independent Self-Assembly of Germ Granule mRNAs into Homotypic Clusters. Mol Cell 2020; 78:941-950.e12. [PMID: 32464092 DOI: 10.1016/j.molcel.2020.05.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/29/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022]
Abstract
mRNAs enriched in membraneless condensates provide functional compartmentalization within cells. The mechanisms that recruit transcripts to condensates are under intense study; however, how mRNAs organize once they reach a granule remains poorly understood. Here, we report on a self-sorting mechanism by which multiple mRNAs derived from the same gene assemble into discrete homotypic clusters. We demonstrate that in vivo mRNA localization to granules and self-assembly within granules are governed by different mRNA features: localization is encoded by specific RNA regions, whereas self-assembly involves the entire mRNA, does not involve sequence-specific, ordered intermolecular RNA:RNA interactions, and is thus RNA sequence independent. We propose that the ability of mRNAs to self-sort into homotypic assemblies is an inherent property of an messenger ribonucleoprotein (mRNP) that is augmented under conditions that increase RNA concentration, such as upon enrichment in RNA-protein granules, a process that appears conserved in diverse cellular contexts and organisms.
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Affiliation(s)
- Tatjana Trcek
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA.
| | - Tyler E Douglas
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA
| | - Markus Grosch
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA
| | - Yandong Yin
- Department of Biochemistry and Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Whitby V I Eagle
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Elizabeth R Gavis
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD, USA
| | - Eli Rothenberg
- Department of Biochemistry and Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Ruth Lehmann
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA.
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31
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Rey-Suarez I, Wheatley BA, Koo P, Bhanja A, Shu Z, Mochrie S, Song W, Shroff H, Upadhyaya A. WASP family proteins regulate the mobility of the B cell receptor during signaling activation. Nat Commun 2020; 11:439. [PMID: 31974357 PMCID: PMC6978525 DOI: 10.1038/s41467-020-14335-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022] Open
Abstract
Regulation of membrane receptor mobility tunes cellular response to external signals, such as in binding of B cell receptors (BCR) to antigen, which initiates signaling. However, whether BCR signaling is regulated by BCR mobility, and what factors mediate this regulation, are not well understood. Here we use single molecule imaging to examine BCR movement during signaling activation and a novel machine learning method to classify BCR trajectories into distinct diffusive states. Inhibition of actin dynamics downstream of the actin nucleating factors, Arp2/3 and formin, decreases BCR mobility. Constitutive loss or acute inhibition of the Arp2/3 regulator, N-WASP, which is associated with enhanced signaling, increases the proportion of BCR trajectories with lower diffusivity. Furthermore, loss of N-WASP reduces the diffusivity of CD19, a stimulatory co-receptor, but not that of FcγRIIB, an inhibitory co-receptor. Our results implicate a dynamic actin network in fine-tuning receptor mobility and receptor-ligand interactions for modulating B cell signaling. B cell receptors (BCR) capture antigen and initiate downstream antibody responses, but whether and how BCR signaling is regulated by BCR mobility is still unclear. Here the authors show, using single molecule imaging and machine learning analyses, that BCR and CD19 mobility is modulated by the actin nucleation regulators Arp2/3 and N-WASP to control BCR signaling.
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Affiliation(s)
- Ivan Rey-Suarez
- Biophysics Program, University of Maryland, College Park, MD, 20742, USA.,National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Brittany A Wheatley
- Department of Physics, University of Maryland, College Park, MD, 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD, 20742, USA
| | - Peter Koo
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Anshuman Bhanja
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Zhou Shu
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.,Division of Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Simon Mochrie
- Department of Physics, Yale University, New Haven, CT, 06520, USA
| | - Wenxia Song
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Hari Shroff
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Arpita Upadhyaya
- Biophysics Program, University of Maryland, College Park, MD, 20742, USA. .,Department of Physics, University of Maryland, College Park, MD, 20742, USA. .,Institute for Physical Science and Technology, University of Maryland, College Park, MD, 20742, USA.
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32
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Bhagwat AR, Le Sage V, Nturibi E, Kulej K, Jones J, Guo M, Tae Kim E, Garcia BA, Weitzman MD, Shroff H, Lakdawala SS. Quantitative live cell imaging reveals influenza virus manipulation of Rab11A transport through reduced dynein association. Nat Commun 2020; 11:23. [PMID: 31911620 PMCID: PMC6946661 DOI: 10.1038/s41467-019-13838-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 11/20/2019] [Indexed: 11/10/2022] Open
Abstract
Assembly of infectious influenza A viruses (IAV) is a complex process involving transport from the nucleus to the plasma membrane. Rab11A-containing recycling endosomes have been identified as a platform for intracellular transport of viral RNA (vRNA). Here, using high spatiotemporal resolution light-sheet microscopy (~1.4 volumes/second, 330 nm isotropic resolution), we quantify Rab11A and vRNA movement in live cells during IAV infection and report that IAV infection decreases speed and increases arrest of Rab11A. Unexpectedly, infection with respiratory syncytial virus alters Rab11A motion in a manner opposite to IAV, suggesting that Rab11A is a common host component that is differentially manipulated by respiratory RNA viruses. Using two-color imaging we demonstrate co-transport of Rab11A and IAV vRNA in infected cells and provide direct evidence that vRNA-associated Rab11A have altered transport. The mechanism of altered Rab11A movement is likely related to a decrease in dynein motors bound to Rab11A vesicles during IAV infection.
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Affiliation(s)
- Amar R Bhagwat
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Valerie Le Sage
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Eric Nturibi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Katarzyna Kulej
- The Children's Hospital of Philadelphia Research Institute, 3501 Civic Center Dr., Philadelphia, PA, 19104, USA
| | - Jennifer Jones
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Min Guo
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Building 13, Bethesda, MD, 20892, USA
| | - Eui Tae Kim
- The Children's Hospital of Philadelphia Research Institute, 3501 Civic Center Dr., Philadelphia, PA, 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA, 19104, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, 3400, Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Matthew D Weitzman
- The Children's Hospital of Philadelphia Research Institute, 3501 Civic Center Dr., Philadelphia, PA, 19104, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, 3400, Civic Center Blvd, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Building 13, Bethesda, MD, 20892, USA
| | - Seema S Lakdawala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA.
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA.
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33
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Markwardt ML, Snell NE, Guo M, Wu Y, Christensen R, Liu H, Shroff H, Rizzo MA. A Genetically Encoded Biosensor Strategy for Quantifying Non-muscle Myosin II Phosphorylation Dynamics in Living Cells and Organisms. Cell Rep 2020; 24:1060-1070.e4. [PMID: 30044973 PMCID: PMC6117825 DOI: 10.1016/j.celrep.2018.06.088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 05/25/2018] [Accepted: 06/20/2018] [Indexed: 02/06/2023] Open
Abstract
Complex cell behaviors require dynamic control over non-muscle myosin II (NMMII) regulatory light chain (RLC) phosphorylation. Here, we report that RLC phosphorylation can be tracked in living cells and organisms using a homotransfer fluorescence resonance energy transfer (FRET) approach. Fluorescent protein-tagged RLCs exhibit FRET in the dephosphorylated conformation, permitting identification and quantification of RLC phosphorylation in living cells. This approach is versatile and can accommodate several different fluorescent protein colors, thus enabling multiplexed imaging with complementary biosensors. In fibroblasts, dynamic myosin phosphorylation was observed at the leading edge of migrating cells and retracting structures where it persistently colocalized with activated myosin light chain kinase. Changes in myosin phosphorylation during C. elegans embryonic development were tracked using polarization inverted selective-plane illumination microscopy (piSPIM), revealing a shift in phosphorylated myosin localization to a longitudinal orientation following the onset of twitching. Quantitative analyses further suggested that RLC phosphorylation dynamics occur independently from changes in protein expression. Markwardt et al. report a myosin II phosphorylation assay based on homotransfer between fluorescent protein-tagged regulatory light chains. This approach was used to track the dynamics of myosin phosphorylation in migrating fibroblasts. Quantitative polarization imaging was also fused with light sheet microscopy to follow myosin phosphorylation in developing C. elegans.
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Affiliation(s)
- Michele L Markwardt
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nicole E Snell
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Min Guo
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, US NIH, Bethesda, MD 20814, USA
| | - Yicong Wu
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, US NIH, Bethesda, MD 20814, USA
| | - Ryan Christensen
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, US NIH, Bethesda, MD 20814, USA
| | - Huafeng Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, US NIH, Bethesda, MD 20814, USA
| | - M A Rizzo
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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34
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Abstract
We propose a network of National Imaging Centers that provide collaborative, interdisciplinary spaces needed for developing, applying and teaching advanced biological imaging techniques. Our proposal is based on recommendations from an NSF sponsored workshop on realizing the promise of innovations in imaging and computation for biological discovery.
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Affiliation(s)
- Daniel A Colón-Ramos
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Instituto de Neurobiología, Recinto de Ciencias Médicas, Universidad de Puerto Rico, San Juan, Puerto Rico, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
| | - Patrick La Riviere
- Marine Biological Laboratory, Woods Hole, MA, USA
- Department of Radiology, University of Chicago, Chicago, IL, USA
| | - Hari Shroff
- Marine Biological Laboratory, Woods Hole, MA, USA
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
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35
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Duncan LH, Moyle MW, Shao L, Sengupta T, Ikegami R, Kumar A, Guo M, Christensen R, Santella A, Bao Z, Shroff H, Mohler W, Colón-Ramos DA. Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution. J Vis Exp 2019. [PMID: 31233035 DOI: 10.3791/59533] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Caenorhabditis elegans (C. elegans) stands out as the only organism in which the challenge of understanding the cellular origins of an entire nervous system can be observed, with single cell resolution, in vivo. Here, we present an integrated protocol for the examination of neurodevelopment in C. elegans embryos. Our protocol combines imaging, lineaging and neuroanatomical tracing of single cells in developing embryos. We achieve long-term, four-dimensional (4D) imaging of living C. elegans embryos with nearly isotropic spatial resolution through the use of Dual-view Inverted Selective Plane Illumination Microscopy (diSPIM). Nuclei and neuronal structures in the nematode embryos are imaged and isotropically fused to yield images with resolution of ~330 nm in all three dimensions. These minute-by-minute high-resolution 4D data sets are then analyzed to correlate definitive cell-lineage identities with gene expression and morphological dynamics at single-cell and subcellular levels of detail. Our protocol is structured to enable modular implementation of each of the described steps and enhance studies on embryogenesis, gene expression, or neurodevelopment.
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Affiliation(s)
- Leighton H Duncan
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org
| | - Mark W Moyle
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org
| | - Lin Shao
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org
| | - Titas Sengupta
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org
| | - Richard Ikegami
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org
| | - Abhishek Kumar
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health; WormGUIDES.org
| | - Min Guo
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health; WormGUIDES.org
| | - Ryan Christensen
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health; WormGUIDES.org
| | - Anthony Santella
- Developmental Biology Program, Sloan Kettering Institute; WormGUIDES.org
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute; WormGUIDES.org
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health; WormGUIDES.org
| | - William Mohler
- Department of Genetics and Genome Sciences and Center for Cell Analysis and Modeling, University of Connecticut Health Center; WormGUIDES.org;
| | - Daniel A Colón-Ramos
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org; Instituto de Neurobiología, Recinto de Ciencias Médicas, Universidad de Puerto Rico;
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Vogt EJ, Tokuhiro K, Guo M, Dale R, Yang G, Shin SW, Movilla MJ, Shroff H, Dean J. Anchoring cortical granules in the cortex ensures trafficking to the plasma membrane for post-fertilization exocytosis. Nat Commun 2019; 10:2271. [PMID: 31118423 PMCID: PMC6531442 DOI: 10.1038/s41467-019-10171-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 04/24/2019] [Indexed: 01/13/2023] Open
Abstract
Following fertilization, cortical granules exocytose ovastacin, a metalloendopeptidase that cleaves ZP2 in the zona pellucida surrounding mouse eggs to prevent additional sperm binding. Using high- and super-resolution imaging with ovastacinmCherry as a fluorescent marker, we characterize cortical granule dynamics at single granule resolution in transgenic mouse eggs. Newly-developed imaging protocols provide an unprecedented view of vesicular dynamics near the plasma membrane in mouse eggs. We discover that cortical granule anchoring in the cortex is dependent on maternal MATER and document that myosin IIA is required for biphasic trafficking to the plasma membrane. We observe local clearance of cortical actin during exocytosis and determine that pharmacologic or genetic disruption of trafficking to the plasma membrane impairs secretion of cortical granules and results in polyspermy. Thus, the regulation of cortical granule dynamics at the cortex-plasma membrane interface is critical for exocytosis and the post-fertilization block to sperm binding that ensures monospermic fertilization.
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Affiliation(s)
- Edgar-John Vogt
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD, 20892, USA
- Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Keizo Tokuhiro
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Genome Editing, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shinmachi, Hirakata, Osaka, 573-1010, Japan
| | - Min Guo
- Section on High Resolution Optical Imaging, NIBIB, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ryan Dale
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD, 20892, USA
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Guanghui Yang
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Seung-Wook Shin
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Maria Jimenez Movilla
- Department of Cell Biology and Histology, Medical School, University of Murcia, IMIB, 30100, Murcia, Spain
| | - Hari Shroff
- Section on High Resolution Optical Imaging, NIBIB, National Institutes of Health, Bethesda, MD, 20892, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD, 20892, USA.
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37
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Alfonzo Mendez MA, Viswasrao H, Shroff H, Taraska JW. 3D Trafficking of Epidermal Growth Factor Receptor in Live Cells. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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38
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Christensen R, Bokinsky A, Santella A, Moyle M, Guo M, Lauziere A, Ardiel E, Vishwasrao HD, Harvey B, Levin M, Karaj N, Mohler W, Daniel Colón-Ramos D, Bao Z, Shroff H. Generating a 4D Atlas of Nuclear Positions in Embryonic Caenorhabditis elegans. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.3001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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39
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Wu Y, Shroff H. Faster, sharper, and deeper: structured illumination microscopy for biological imaging. Nat Methods 2018; 15:1011-1019. [PMID: 30478322 DOI: 10.1038/s41592-018-0211-z] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/02/2018] [Indexed: 11/09/2022]
Abstract
Structured illumination microscopy (SIM) allows rapid, super-resolution (SR) imaging in live specimens. We review recent technical advances in SR-SIM, with emphasis on imaging speed, resolution, and depth. Since its introduction decades ago, the technique has grown to offer myriad implementations, each with its own strengths and weaknesses. We discuss these, aiming to provide a practical guide for biologists and to highlight which approach is best suited to a given application.
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Affiliation(s)
- Yicong Wu
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
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40
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Xu M, Wu Y, Shroff H, Wu M, Mani M. A scheme for 3-dimensional morphological reconstruction and force inference in the early C. elegans embryo. PLoS One 2018; 13:e0199151. [PMID: 29990323 PMCID: PMC6038995 DOI: 10.1371/journal.pone.0199151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/03/2018] [Indexed: 11/19/2022] Open
Abstract
In this study, we present a scheme for the reconstruction of cellular morphology and the inference of mechanical forces in the early C. elegans embryo. We have developed and bench-marked a morphological reconstruction scheme that transforms flourescence-based in vivo images of membranes into a point cloud of smoothed surface patches, which facilitates an accurate estimation of membrane curvatures and the angles between membranes. Assuming an isotropic and homogeneous distribution of tensions along individual membranes, we infer a pattern of forces that are 7% deviated from force balance at edges, and 10% deviated from the Young-Laplace relation across membranes. We demonstrate the stability of our inference scheme via a sensitivity analysis, and the reproducibility of our image-analysis and force inference pipelines.
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Affiliation(s)
- Muzhi Xu
- Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, United States of America
| | - Yicong Wu
- Section on High Resolution Optical Imaging, NIBIB, NIH, Bethesda, Maryland 20892, United States of America
| | - Hari Shroff
- Section on High Resolution Optical Imaging, NIBIB, NIH, Bethesda, Maryland 20892, United States of America
| | - Min Wu
- Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, United States of America
- Mathematical Sciences, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States of America
| | - Madhav Mani
- Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, United States of America
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States of America
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41
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Guo M, Chandris P, Giannini JP, Trexler AJ, Fischer R, Chen J, Vishwasrao HD, Rey-Suarez I, Wu Y, Wu X, Waterman CM, Patterson GH, Upadhyaya A, Taraska JW, Shroff H. Single-shot super-resolution total internal reflection fluorescence microscopy. Nat Methods 2018; 15:425-428. [PMID: 29735999 PMCID: PMC7470603 DOI: 10.1038/s41592-018-0004-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/18/2018] [Indexed: 12/21/2022]
Abstract
We combined instant structured illumination microscopy (iSIM) with total internal reflection fluorescence microscopy (TIRFM) in an approach referred to as instant TIRF-SIM, thereby improving the lateral spatial resolution of TIRFM to 115 ± 13 nm without compromising speed, and enabling imaging frame rates up to 100 Hz over hundreds of time points. We applied instant TIRF-SIM to multiple live samples and achieved rapid, high-contrast super-resolution imaging close to the coverslip surface.
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Affiliation(s)
- Min Guo
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
| | - Panagiotis Chandris
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - John Paul Giannini
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Biophysics Program, University of Maryland, College Park, MD, USA
| | - Adam J Trexler
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Northrop Grumman Corporation, Monterey, CA, USA
| | - Robert Fischer
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Ivan Rey-Suarez
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Biophysics Program, University of Maryland, College Park, MD, USA
| | - Yicong Wu
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Xufeng Wu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clare M Waterman
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - George H Patterson
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Arpita Upadhyaya
- Department of Physics and Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Justin W Taraska
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Department of Physics and Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
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42
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Traver MK, Campanello L, Huaman C, Paul S, Shroff H, Losert W, Schaefer BC. A transient Malt1 aggresome sustains T cell receptor signaling to NF-κB. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.112.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The T cell receptor (TCR) to NF-κB signaling pathway is crucial for T cell activation and differentiation. Upon engagement of the TCR with cognate antigen, a series of events leads to the formation of the Carma1-Bcl10-Malt1 (CBM) complex, increasingly recognized as vital to a properly functioning immune response. We have demonstrated that in effector T cells, the CBM complex gives rise to a polymeric, filamentous signalosome called POLKADOTS that directs terminal activation of NF-κB. POLKADOTS consist of the core protein Bcl10, its constitutive binding partner Malt1, and their recruited signaling partners. We have previously shown that Bcl10 is degraded via selective autophagy following T cell activation. Here, we show that Malt1, which serves both as an adaptor transmitting signals to NF-κB and as a protease which cleaves a variety of substrates, is not concurrently degraded. Instead, Malt1-containing POLKADOTS coalesce via microtubule transport to a canonical aggresome. Aggresomes are thought to be depots of misfolded protein destined for degradation via macroautophagy; however, the Malt1 aggresome promotes late stage NF-κB activation through prolonging pIKK-Malt1 interactions. Additionally, this aggresome enhances the proteolysis of a subset of Malt1 targets. These results establish a mechanism for sustaining cytoplasmic signals from the TCR. More broadly, our findings demonstrate that aggresomes can serve as a stable platform for signal transduction.
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43
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Ogawa M, Tomita Y, Nakamura Y, Lee MJ, Lee S, Tomita S, Nagaya T, Sato K, Yamauchi T, Iwai H, Kumar A, Haystead T, Shroff H, Choyke PL, Trepel JB, Kobayashi H. Immunogenic cancer cell death selectively induced by near infrared photoimmunotherapy initiates host tumor immunity. Oncotarget 2018; 8:10425-10436. [PMID: 28060726 PMCID: PMC5354669 DOI: 10.18632/oncotarget.14425] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/13/2016] [Indexed: 01/20/2023] Open
Abstract
Immunogenic cell death (ICD) is a form of cell death that activates an adaptive immune response against dead-cell-associated antigens. Cancer cells killed via ICD can elicit antitumor immunity. ICD is efficiently induced by near-infrared photo-immunotherapy (NIR-PIT) that selectively kills target-cells on which antibody-photoabsorber conjugates bind and are activated by NIR light exposure. Advanced live cell microscopies showed that NIR-PIT caused rapid and irreversible damage to the cell membrane function leading to swelling and bursting, releasing intracellular components due to the influx of water into the cell. The process also induces relocation of ICD bio markers including calreticulin, Hsp70 and Hsp90 to the cell surface and the rapid release of immunogenic signals including ATP and HMGB1 followed by maturation of immature dendritic cells. Thus, NIR-PIT is a therapy that kills tumor cells by ICD, eliciting a host immune response against tumor.
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Affiliation(s)
- Mikako Ogawa
- Medical Photonics Research Center, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan.,Laboratory for Bioanalysis and Molecular Imaging, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Yusuke Tomita
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yuko Nakamura
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Min-Jung Lee
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sunmin Lee
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Saori Tomita
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Tadanobu Nagaya
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Kazuhide Sato
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Toyohiko Yamauchi
- Central Research Laboratory, Hamamatsu Photonics K. K., Hamamatsu 434-8601, Japan
| | - Hidenao Iwai
- Central Research Laboratory, Hamamatsu Photonics K. K., Hamamatsu 434-8601, Japan
| | - Abhishek Kumar
- Section on High Resolution Optical Imaging, NIBIB/NIH, Bethesda, MD 20892, USA
| | - Timothy Haystead
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, NIBIB/NIH, Bethesda, MD 20892, USA
| | - Peter L Choyke
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jane B Trepel
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Hisataka Kobayashi
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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44
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Affiliation(s)
- Christian A. Combs
- NHLBI Light Microscopy Facility, National Institutes of Health Bethesda Maryland
| | - Hari Shroff
- NIBIB Section on High Resolution Optical Imaging, National Institutes of Health Bethesda Maryland
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45
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Chandler T, Mehta S, Shroff H, Oldenbourg R, La Rivière PJ. Single-fluorophore orientation determination with multiview polarized illumination: modeling and microscope design. Opt Express 2017; 25:31309-31325. [PMID: 29245807 PMCID: PMC5941992 DOI: 10.1364/oe.25.031309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/13/2017] [Accepted: 11/23/2017] [Indexed: 06/02/2023]
Abstract
We investigate the use of polarized illumination in multiview microscopes for determining the orientation of single-molecule fluorescence transition dipoles. First, we relate the orientation of single dipoles to measurable intensities in multiview microscopes and develop an information-theoretic metric-the solid-angle uncertainty-to compare the ability of multiview microscopes to estimate the orientation of single dipoles. Next, we compare a broad class of microscopes using this metric-single- and dual-view microscopes with varying illumination polarization, illumination numerical aperture (NA), detection NA, obliquity, asymmetry, and exposure. We find that multi-view microscopes can measure all dipole orientations, while the orientations measurable with single-view microscopes is halved because of symmetries in the detection process. We also find that choosing a small illumination NA and a large detection NA are good design choices, that multiview microscopes can benefit from oblique illumination and detection, and that asymmetric NA microscopes can benefit from exposure asymmetry.
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Affiliation(s)
- Talon Chandler
- University of Chicago, Department of Radiology, Chicago, Illinois 60637,
USA
| | - Shalin Mehta
- University of Chicago, Department of Radiology, Chicago, Illinois 60637,
USA
- Marine Biological Laboratory, Bell Center, Woods Hole, Massachusetts 02543,
USA
- (present address) Chan Zuckerberg Biohub, San Francisco, California 94158,
USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892,
USA
- Marine Biological Laboratory, Whitman Center, Woods Hole, Massachusetts 02543,
USA
| | - Rudolf Oldenbourg
- Marine Biological Laboratory, Bell Center, Woods Hole, Massachusetts 02543,
USA
- Brown University, Department of Physics, Providence, Rhode Island 02912,
USA
| | - Patrick J. La Rivière
- University of Chicago, Department of Radiology, Chicago, Illinois 60637,
USA
- Marine Biological Laboratory, Whitman Center, Woods Hole, Massachusetts 02543,
USA
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46
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Zhu G, Lynn GM, Jacobson O, Chen K, Liu Y, Zhang H, Ma Y, Zhang F, Tian R, Ni Q, Cheng S, Wang Z, Lu N, Yung BC, Wang Z, Lang L, Fu X, Jin A, Weiss ID, Vishwasrao H, Niu G, Shroff H, Klinman DM, Seder RA, Chen X. Albumin/vaccine nanocomplexes that assemble in vivo for combination cancer immunotherapy. Nat Commun 2017; 8:1954. [PMID: 29203865 PMCID: PMC5715147 DOI: 10.1038/s41467-017-02191-y] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/13/2017] [Indexed: 01/09/2023] Open
Abstract
Subunit vaccines have been investigated in over 1000 clinical trials of cancer immunotherapy, but have shown limited efficacy. Nanovaccines may improve efficacy but have rarely been clinically translated. By conjugating molecular vaccines with Evans blue (EB) into albumin-binding vaccines (AlbiVax), here we develop clinically promising albumin/AlbiVax nanocomplexes that self-assemble in vivo from AlbiVax and endogenous albumin for efficient vaccine delivery and potent cancer immunotherapy. PET pharmacoimaging, super-resolution microscopies, and flow cytometry reveal almost 100-fold more efficient co-delivery of CpG and antigens (Ags) to lymph nodes (LNs) by albumin/AlbiVax than benchmark incomplete Freund's adjuvant (IFA). Albumin/AlbiVax elicits ~10 times more frequent peripheral antigen-specific CD8+ cytotoxic T lymphocytes with immune memory than IFA-emulsifying vaccines. Albumin/AlbiVax specifically inhibits progression of established primary or metastatic EG7.OVA, B16F10, and MC38 tumors; combination with anti-PD-1 and/or Abraxane further potentiates immunotherapy and eradicates most MC38 tumors. Albumin/AlbiVax nanocomplexes are thus a robust platform for combination cancer immunotherapy.
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Affiliation(s)
- Guizhi Zhu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Geoffrey M Lynn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, 20892, USA
| | - Orit Jacobson
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Kai Chen
- Molecular Imaging Center, Department of Radiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Yi Liu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.,School of Engineering, China Pharmaceutical University, Nanjing, 210009, China
| | - Huimin Zhang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Ying Ma
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Fuwu Zhang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Rui Tian
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Qianqian Ni
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Siyuan Cheng
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Zhantong Wang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Nan Lu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Bryant C Yung
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Zhe Wang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Lixin Lang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Xiao Fu
- Laboratory of Cellular Imaging and Macromolecular Biophysics, NIBIB, NIH, Bethesda, MD, 20892, USA
| | - Albert Jin
- Laboratory of Cellular Imaging and Macromolecular Biophysics, NIBIB, NIH, Bethesda, MD, 20892, USA
| | - Ido D Weiss
- Laboratory of Molecular Immunology, NIAID, NIH, Bethesda, MD, 20892, USA
| | - Harshad Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Gang Niu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, 20892, MD, USA.,Section on High Resolution Optical Imaging, NIBIB, NIH, Bethesda, MD, 20892, USA
| | - Dennis M Klinman
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, 20892, USA
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
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47
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Zhu G, Mei L, Vishwasrao HD, Jacobson O, Wang Z, Liu Y, Yung BC, Fu X, Jin A, Niu G, Wang Q, Zhang F, Shroff H, Chen X. Intertwining DNA-RNA nanocapsules loaded with tumor neoantigens as synergistic nanovaccines for cancer immunotherapy. Nat Commun 2017; 8:1482. [PMID: 29133898 PMCID: PMC5684198 DOI: 10.1038/s41467-017-01386-7] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/14/2017] [Indexed: 01/05/2023] Open
Abstract
Nanomedicines that co-deliver DNA, RNA, and peptide therapeutics are highly desirable yet remain underdeveloped for cancer theranostics. Herein, we report self-assembled intertwining DNA-RNA nanocapsules (iDR-NCs) that efficiently delivered synergistic DNA CpG and short hairpin RNA (shRNA) adjuvants, as well as tumor-specific peptide neoantigens into antigen presenting cells (APCs) in lymph nodes for cancer immunotherapy. These nanovaccines were prepared by (1) producing tandem CpG and shRNA via concurrent rolling circle replication and rolling circle transcription, (2) self-assembling CpG and shRNA into DNA-RNA microflowers, (3) shrinking microflowers into iDR-NCs using PEG-grafted cationic polypeptides, and (4) physically loading neoantigen into iDR-NCs. CpG and shRNA in iDR-NCs synergistically activate APCs for sustained antigen presentation. Remarkably, iDR-NC/neoantigen nanovaccines elicit 8-fold more frequent neoantigen-specific peripheral CD8+ T cells than CpG, induce T cell memory, and significantly inhibit the progression of neoantigen-specific colorectal tumors. Collectively, iDR-NCs represent potential DNA/RNA/peptide triple-co-delivery nanocarriers and synergistic tumor immunotherapeutic nanovaccines. Nucleic acid nanomedicines are promising for cancer drug delivery. Here, the authors show using a mouse model the tumor immunotherapeutic efficacy of nanovaccines based on intertwining DNA-RNA nanocapsules loaded with DNA CpG, Stat3-silencing short hairpin RNA and tumor-specific peptide neoantigens.
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Affiliation(s)
- Guizhi Zhu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Lei Mei
- Department of Nutrition and Food Science, College of Agriculture and Natural Resources, University of Maryland, College Park, MD, 20742, USA
| | | | - Orit Jacobson
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Zhantong Wang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Yijing Liu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Bryant C Yung
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Xiao Fu
- Laboratory of Cellular Imaging and Macromolecular Biophysics, NIBIB, NIH, Bethesda, MD, 20892, USA
| | - Albert Jin
- Laboratory of Cellular Imaging and Macromolecular Biophysics, NIBIB, NIH, Bethesda, MD, 20892, USA
| | - Gang Niu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Qin Wang
- Department of Nutrition and Food Science, College of Agriculture and Natural Resources, University of Maryland, College Park, MD, 20742, USA
| | - Fuwu Zhang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, NIH, Bethesda, MD, 20892, USA.,Section on High Resolution Optical Imaging, NIBIB, NIH, Bethesda, MD, 20892, USA
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
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48
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Wu Y, Kumar A, Smith C, Ardiel E, Chandris P, Christensen R, Rey-Suarez I, Guo M, Vishwasrao HD, Chen J, Tang J, Upadhyaya A, La Riviere PJ, Shroff H. Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy. Nat Commun 2017; 8:1452. [PMID: 29129912 PMCID: PMC5682293 DOI: 10.1038/s41467-017-01250-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/31/2017] [Indexed: 11/09/2022] Open
Abstract
Light-sheet fluorescence microscopy (LSFM) enables high-speed, high-resolution, and gentle imaging of live specimens over extended periods. Here we describe a technique that improves the spatiotemporal resolution and collection efficiency of LSFM without modifying the underlying microscope. By imaging samples on reflective coverslips, we enable simultaneous collection of four complementary views in 250 ms, doubling speed and improving information content relative to symmetric dual-view LSFM. We also report a modified deconvolution algorithm that removes associated epifluorescence contamination and fuses all views for resolution recovery. Furthermore, we enhance spatial resolution (to <300 nm in all three dimensions) by applying our method to single-view LSFM, permitting simultaneous acquisition of two high-resolution views otherwise difficult to obtain due to steric constraints at high numerical aperture. We demonstrate the broad applicability of our method in a variety of samples, studying mitochondrial, membrane, Golgi, and microtubule dynamics in cells and calcium activity in nematode embryos.
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Affiliation(s)
- Yicong Wu
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA.
| | - Abhishek Kumar
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Corey Smith
- Department of Radiology, University of Chicago, Chicago, 60637, Illinois, USA
| | - Evan Ardiel
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Panagiotis Chandris
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Ryan Christensen
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Ivan Rey-Suarez
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA.,Biophysics Program, University of Maryland, College Park, 02543, Maryland, USA
| | - Min Guo
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Jianyong Tang
- JT Scientific Consulting LLC, North Potomac, 20878, Maryland, USA
| | - Arpita Upadhyaya
- Biophysics Program, University of Maryland, College Park, 02543, Maryland, USA.,Department of Physics and Institute of Physical Science and Technology, University of Maryland, College Park, 20740, Maryland, USA
| | - Patrick J La Riviere
- Department of Radiology, University of Chicago, Chicago, 60637, Illinois, USA.,Whitman Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA.,Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, 20892, Maryland, USA.,Department of Physics and Institute of Physical Science and Technology, University of Maryland, College Park, 20740, Maryland, USA.,Whitman Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
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49
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Giannini JP, York AG, Shroff H. Anticipating, measuring, and minimizing MEMS mirror scan error to improve laser scanning microscopy's speed and accuracy. PLoS One 2017; 12:e0185849. [PMID: 28973013 PMCID: PMC5626505 DOI: 10.1371/journal.pone.0185849] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/20/2017] [Indexed: 11/18/2022] Open
Abstract
We describe a method to speed up microelectromechanical system (MEMS) mirror scanning by > 20x, while also improving scan accuracy. We use Landweber deconvolution to determine an input voltage which would produce a desired output, based on the measured MEMS impulse response. Since the MEMS is weakly nonlinear, the observed behavior deviates from expectations, and we iteratively improve our input to minimize this deviation. This allows customizable MEMS angle vs. time with <1% deviation from the desired scan pattern. We demonstrate our technique by optimizing a point scanning microscope's raster patterns to image mammal submandibular gland and pollen at ~10 frames/s.
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Affiliation(s)
- John P. Giannini
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
- Biophysics Program, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
| | - Andrew G. York
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
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50
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Sardo L, Lin A, Khakhina S, Beckman L, Ricon L, Elbezanti W, Jaison T, Vishwasrao H, Shroff H, Janetopoulos C, Klase ZA. Real-time visualization of chromatin modification in isolated nuclei. J Cell Sci 2017; 130:2926-2940. [PMID: 28743737 PMCID: PMC5612227 DOI: 10.1242/jcs.205823] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/13/2017] [Indexed: 12/31/2022] Open
Abstract
Chromatin modification is traditionally assessed in biochemical assays that provide average measurements of static events given that the analysis requires components from many cells. Microscopy can visualize single cells, but the cell body and organelles can hamper staining and visualization of the nucleus. Normally, chromatin is visualized by immunostaining a fixed sample or by expressing exogenous fluorescently tagged proteins in a live cell. Alternative microscopy tools to observe changes of endogenous chromatin in real-time are needed. Here, we isolated transcriptionally competent nuclei from cells and used antibody staining without fixation to visualize changes in endogenous chromatin. This method allows the real-time addition of drugs and fluorescent probes to one or more nuclei while under microscopy observation. A high-resolution map of 11 endogenous nuclear markers of the histone code, transcription machinery and architecture was obtained in transcriptionally active nuclei by performing confocal and structured illumination microscopy. We detected changes in chromatin modification and localization at the single-nucleus level after inhibition of histone deacetylation. Applications in the study of RNA transcription, viral protein function and nuclear architecture are presented. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Luca Sardo
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Angel Lin
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Svetlana Khakhina
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Lucas Beckman
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Luis Ricon
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Weam Elbezanti
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Tara Jaison
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Harshad Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 28092, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 28092, USA
| | - Christopher Janetopoulos
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Zachary A Klase
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
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