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18 results on '"Yu, Chih-Chieh Jay"'

1. Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator

Author

Shemesh, Or A, Linghu, Changyang, Piatkevich, Kiryl D, Goodwin, Daniel, Celiker, Orhan Tunc, Gritton, Howard J, Romano, Michael F, Gao, Ruixuan, Yu, Chih-Chieh Jay, Tseng, Hua-An, Bensussen, Seth, Narayan, Sujatha, Yang, Chao-Tsung, Freifeld, Limor, Siciliano, Cody A, Gupta, Ishan, Wang, Joyce, Pak, Nikita, Yoon, Young-Gyu, Ullmann, Jeremy FP, Guner-Ataman, Burcu, Noamany, Habiba, Sheinkopf, Zoe R, Park, Won Min, Asano, Shoh, Keating, Amy E, Trimmer, James S, Reimer, Jacob, Tolias, Andreas S, Bear, Mark F, Tye, Kay M, Han, Xue, Ahrens, Misha B, and Boyden, Edward S

Subjects
Neurosciences, Bioengineering, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Animals, Artifacts, Brain, Calcium, Calcium-Binding Proteins, Cell Body, Green Fluorescent Proteins, Mice, Neurons, Neuropil, Optical Imaging, Zebrafish, GCaMP6, GCaMP7, calcium imaging, correlation, crosstalk, in vivo imaging, microscopy, neuropil contamination, soma-targeting, two-photon microscopy, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

Methods for one-photon fluorescent imaging of calcium dynamics can capture the activity of hundreds of neurons across large fields of view at a low equipment complexity and cost. In contrast to two-photon methods, however, one-photon methods suffer from higher levels of crosstalk from neuropil, resulting in a decreased signal-to-noise ratio and artifactual correlations of neural activity. We address this problem by engineering cell-body-targeted variants of the fluorescent calcium indicators GCaMP6f and GCaMP7f. We screened fusions of GCaMP to natural, as well as artificial, peptides and identified fusions that localized GCaMP to within 50 μm of the cell body of neurons in mice and larval zebrafish. One-photon imaging of soma-targeted GCaMP in dense neural circuits reported fewer artifactual spikes from neuropil, an increased signal-to-noise ratio, and decreased artifactual correlation across neurons. Thus, soma-targeting of fluorescent calcium indicators facilitates usage of simple, powerful, one-photon methods for imaging neural calcium dynamics.

Published
2020

3. Improved immunostaining of nanostructures and cells in human brain specimens through expansion-mediated protein decrowding

Author

Valdes, Pablo A., primary, Yu, Chih-Chieh (Jay), additional, Aronson, Jenna, additional, Ghosh, Debarati, additional, Zhao, Yongxin, additional, An, Bobae, additional, Bernstock, Joshua D., additional, Bhere, Deepak, additional, Felicella, Michelle M., additional, Viapiano, Mariano S., additional, Shah, Khalid, additional, Chiocca, E. Antonio, additional, and Boyden, Edward S., additional

Published
2024
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4. Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator

Author

Shemesh, Or A., Linghu, Changyang, Piatkevich, Kiryl D., Goodwin, Daniel, Celiker, Orhan Tunc, Gritton, Howard J., Romano, Michael F., Gao, Ruixuan, Yu, Chih-Chieh (Jay), Tseng, Hua-An, Bensussen, Seth, Narayan, Sujatha, Yang, Chao-Tsung, Freifeld, Limor, Siciliano, Cody A., Gupta, Ishan, Wang, Joyce, Pak, Nikita, Yoon, Young-Gyu, Ullmann, Jeremy F.P., Guner-Ataman, Burcu, Noamany, Habiba, Sheinkopf, Zoe R., Park, Won Min, Asano, Shoh, Keating, Amy E., Trimmer, James S., Reimer, Jacob, Tolias, Andreas S., Bear, Mark F., Tye, Kay M., Han, Xue, Ahrens, Misha B., Boyden, Edward S., Shemesh, Or A., Linghu, Changyang, Piatkevich, Kiryl D., Goodwin, Daniel, Celiker, Orhan Tunc, Gritton, Howard J., Romano, Michael F., Gao, Ruixuan, Yu, Chih-Chieh (Jay), Tseng, Hua-An, Bensussen, Seth, Narayan, Sujatha, Yang, Chao-Tsung, Freifeld, Limor, Siciliano, Cody A., Gupta, Ishan, Wang, Joyce, Pak, Nikita, Yoon, Young-Gyu, Ullmann, Jeremy F.P., Guner-Ataman, Burcu, Noamany, Habiba, Sheinkopf, Zoe R., Park, Won Min, Asano, Shoh, Keating, Amy E., Trimmer, James S., Reimer, Jacob, Tolias, Andreas S., Bear, Mark F., Tye, Kay M., Han, Xue, Ahrens, Misha B., and Boyden, Edward S.

Abstract

© 2020 Elsevier Inc. One-photon fluorescent imaging of calcium signals can capture the activity of hundreds of neurons across large fields of view but suffers from crosstalk from neuropil. Shemesh et al. engineer cell-body-targeted variants of fluorescent calcium indicators and show in mice and zebrafish that artifactual spikes and correlations are greatly reduced.

Published
2022

5. Photo-expansion microscopy enables super-resolution imaging of cells embedded in 3D hydrogels

Author

Günay, Kemal Arda, Chang, Tze-Ling, Skillin, Nathaniel P., Rao, Varsha V., Macdougall, Laura J., Cutler, Alicia A., Silver, Jason S., Brown, Tobin E., Zhang, Chi, Yu, Chih-Chieh (Jay), Olwin, Bradley B., Boyden, Edward S., and Anseth, Kristi S.

Abstract

Hydrogels are extensively used as tunable, biomimetic three-dimensional cell culture matrices, but optically deep, high-resolution images are often difficult to obtain, limiting nanoscale quantification of cell–matrix interactions and outside-in signalling. Here we present photopolymerized hydrogels for expansion microscopy that enable optical clearance and tunable ×4.6–6.7 homogeneous expansion of not only monolayer cell cultures and tissue sections, but cells embedded within hydrogels. The photopolymerized hydrogels for expansion microscopy formulation relies on a rapid photoinitiated thiol/acrylate mixed-mode polymerization that is not inhibited by oxygen and decouples monomer diffusion from polymerization, which is particularly beneficial when expanding cells embedded within hydrogels. Using this technology, we visualize human mesenchymal stem cells and their interactions with nascently deposited proteins at <120 nm resolution when cultured in proteolytically degradable synthetic polyethylene glycol hydrogels. Results support the notion that focal adhesion maturation requires cellular fibronectin deposition; nuclear deformation precedes cellular spreading; and human mesenchymal stem cells display cell-surface metalloproteinases for matrix remodelling.

Published
2023
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6. Decrowding Expansion Pathology: Unmasking Previously Invisible Nanostructures and Cells in Intact Human Brain Pathology Specimens

Author

Valdes, Pablo A., primary, Yu, Chih-Chieh (Jay), additional, Aronson, Jenna, additional, Zhao, Yongxin, additional, Bernstock, Joshua D., additional, Bhere, Deepak, additional, An, Bobae, additional, Viapiano, Mariano S., additional, Shah, Khalid, additional, Chiocca, E. Antonio, additional, and Boyden, Edward S., additional

Published
2021
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7. Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

Author

Alon, Shahar, Goodwin, Daniel R., Sinha, Anubhav, Wassie, Asmamaw T., Chen, Fei, Daugharthy, Evan R., Bando, Yosuke, Kajita, Atsushi, Xue, Andrew G., Marrett, Karl, Prior, Robert, Cui, Yi, Payne, Andrew C., Yao, Chun-Chen, Suk, Ho-Jun, Wang, Ru, Yu, Chih-Chieh (Jay), Tillberg, Paul, Reginato, Paul, Pak, Nikita, Liu, Songlei, Punthambaker, Sukanya, Iyer, Eswar P. R., Kohman, Richie E., Miller, Jeremy A., Lein, Ed S., Lako, Ana, Cullen, Nicole, Rodig, Scott, Helvie, Karla, Abravanel, Daniel L., Wagle, Nikhil, Johnson, Bruce E., Klughammer, Johanna, Slyper, Michal, Waldman, Julia, Jané-Valbuena, Judit, Rozenblatt-Rosen, Orit, Regev, Aviv, Church, George M., Marblestone, Adam H., Boyden, Edward S., Ali, H. R., Al Sa’d, M., Alon, S., Aparicio, S., Battistoni, G., Balasubramanian, S., Becker, R., Bodenmiller, B., Boyden, E. S., Bressan, D., Bruna, A., Burger, Marcel, Caldas, C., Callari, M., Cannell, I. G., Casbolt, H., Chornay, N., Cui, Y., Dariush, A., Dinh, K., Emenari, A., Eyal-Lubling, Y., Fan, J., Fatemi, A., Fisher, E., González-Solares, E. A., González-Fernández, C., Goodwin, D., Greenwood, W., Grimaldi, F., Hannon, G. J., Harris, O., Harris, S., Jauset, C., Joyce, J. A., Karagiannis, E. D., Kovačević, T., Kuett, L., Kunes, R., Küpcü Yoldaş, A., Lai, D., Laks, E., Lee, H., Lee, M., Lerda, G., Li, Y., McPherson, A., Millar, N., Mulvey, C. M., Nugent, F., O'Flanagan, C. H., Paez-Ribes, M., Pearsall, I., Qosaj, F., Roth, A. J., Rueda, O. M., Ruiz, T., Sawicka, K., Sepúlveda, L. A., Shah, S. P., Shea, A., Sinha, A., Smith, A., Tavaré, S., Tietscher, S., Vázquez-García, I., Vogl, S. L., Walton, N. A., Wassie, A. T., Watson, S. S., Weselak, J., Wild, S. A., Williams, E., Windhager, J., Whitmarsh, T., Xia, C., Zheng, P., and Zhuang, X.

Subjects
In situ, Cell type, Dendritic spine, Sequence analysis, Dendritic Spines, Breast Neoplasms, Computational biology, Biology, Biochemistry, Article, Transcriptome, Mice, 03 medical and health sciences, Animals, Humans, splice, Molecular Biology, Gene, Visual Cortex, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Sequence Analysis, RNA, Gene Expression Profiling, Computational Biology, RNA, Cell Biology, Molecular Imaging, Female, Single-Cell Analysis, Biotechnology
Abstract

Identifying transcript location in cells Identifying where specific RNAs occur within a cell or tissue has been limited by technology and imaging capabilities. Expansion microscopy has allowed for better visualization of small structures by expanding the tissues with a polymer- and hydrogel-based system. Alon et al. combined expansion microscopy with long-read in situ RNA sequencing, resulting in a more precise visualization of the location of specific transcripts. This method, termed “ExSeq” for expansion sequencing, was used to detect RNAs, both new transcripts and those previously demonstrated to localize to neuronal dendrites. Unlike other in situ sequencing methods, ExSeq does not target sets of genes. This technology thus unites spatial resolution, multiplexing, and an unbiased approach to reveal insights into RNA localization and its physiological roles in developing and active tissue. Science , this issue p. eaax2656

Published
2021

8. Spatial Multiplexing of Fluorescent Reporters for Imaging Signaling Network Dynamics

Author

Program in Media Arts and Sciences (Massachusetts Institute of Technology), McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology. Center for Neurobiological Engineering, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology. Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Linghu, Changyang, Johnson, Shannon L, Valdes, Pablo A, Shemesh, Or A, Park, Won Min, Park, Demian, Piatkevich, Kiryl D, Wassie, Asmamaw T, Liu, Yixi, An, Bobae, Barnes, Stephanie A, Celiker, Orhan T, Yao, Chun-Chen, Yu, Chih-Chieh Jay, Wang, Ru, Adamala, Katarzyna P, Bear, Mark F, Keating, Amy E, Boyden, Edward S, Program in Media Arts and Sciences (Massachusetts Institute of Technology), McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology. Center for Neurobiological Engineering, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology. Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Linghu, Changyang, Johnson, Shannon L, Valdes, Pablo A, Shemesh, Or A, Park, Won Min, Park, Demian, Piatkevich, Kiryl D, Wassie, Asmamaw T, Liu, Yixi, An, Bobae, Barnes, Stephanie A, Celiker, Orhan T, Yao, Chun-Chen, Yu, Chih-Chieh Jay, Wang, Ru, Adamala, Katarzyna P, Bear, Mark F, Keating, Amy E, and Boyden, Edward S

Abstract

© 2020 The Author(s) In order to analyze how a signal transduction network converts cellular inputs into cellular outputs, ideally one would measure the dynamics of many signals within the network simultaneously. We found that, by fusing a fluorescent reporter to a pair of self-assembling peptides, it could be stably clustered within cells at random points, distant enough to be resolved by a microscope but close enough to spatially sample the relevant biology. Because such clusters, which we call signaling reporter islands (SiRIs), can be modularly designed, they permit a set of fluorescent reporters to be efficiently adapted for simultaneous measurement of multiple nodes of a signal transduction network within single cells. We created SiRIs for indicators of second messengers and kinases and used them, in hippocampal neurons in culture and intact brain slices, to discover relationships between the speed of calcium signaling, and the amplitude of PKA signaling, upon receiving a cAMP-driving stimulus.

Published
2021

9. Expansion microscopy of C. elegans

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Media Laboratory, McGovern Institute for Brain Research at MIT, Harvard University--MIT Division of Health Sciences and Technology, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Yu, Chih-Chieh Jay, Barry, Nicholas C, Wassie, Asmamaw T, Sinha, Anubhav, Bhattacharya, Abhishek, Asano, Shoh, Zhang, Chi, Chen, Fei, Hobert, Oliver, Goodman, Miriam B, Haspel, Gal, Boyden, Edward S, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Media Laboratory, McGovern Institute for Brain Research at MIT, Harvard University--MIT Division of Health Sciences and Technology, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Yu, Chih-Chieh Jay, Barry, Nicholas C, Wassie, Asmamaw T, Sinha, Anubhav, Bhattacharya, Abhishek, Asano, Shoh, Zhang, Chi, Chen, Fei, Hobert, Oliver, Goodman, Miriam B, Haspel, Gal, and Boyden, Edward S

Abstract

© Yu et al. We recently developed expansion microscopy (ExM), which achieves nanoscale-precise imaging of specimens at ~70 nm resolution (with ~4.5x linear expansion) by isotropic swelling of chemically processed, hydrogel-embedded tissue. ExM of C. elegans is challenged by its cuticle, which is stiff and impermeable to antibodies. Here we present a strategy, expansion of C. elegans (ExCel), to expand fixed, intact C. elegans. ExCel enables simultaneous readout of fluorescent proteins, RNA, DNA location, and anatomical structures at resolutions of ~65–75 nm (3.3–3.8x linear expansion). We also developed epitope-preserving ExCel, which enables imaging of endogenous proteins stained by antibodies, and iterative ExCel, which enables imaging of fluorescent proteins after 20x linear expansion. We demonstrate the utility of the ExCel toolbox for mapping synaptic proteins, for identifying previously unreported proteins at cell junctions, and for gene expression analysis in multiple individual neurons of the same animal.

Published
2021

10. Spatial Multiplexing of Fluorescent Reporters for Imaging Signaling Network Dynamics

Author

Linghu, Changyang, primary, Johnson, Shannon L., additional, Valdes, Pablo A., additional, Shemesh, Or A., additional, Park, Won Min, additional, Park, Demian, additional, Piatkevich, Kiryl D., additional, Wassie, Asmamaw T., additional, Liu, Yixi, additional, An, Bobae, additional, Barnes, Stephanie A., additional, Celiker, Orhan T., additional, Yao, Chun-Chen, additional, Yu, Chih-Chieh (Jay), additional, Wang, Ru, additional, Adamala, Katarzyna P., additional, Bear, Mark F., additional, Keating, Amy E., additional, and Boyden, Edward S., additional

Published
2020
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11. Expansion microscopy of C. elegans

Author

Yu, Chih-Chieh (Jay), primary, Barry, Nicholas C, additional, Wassie, Asmamaw T, additional, Sinha, Anubhav, additional, Bhattacharya, Abhishek, additional, Asano, Shoh, additional, Zhang, Chi, additional, Chen, Fei, additional, Hobert, Oliver, additional, Goodman, Miriam B, additional, Haspel, Gal, additional, and Boyden, Edward S, additional

Published
2020
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12. Author response: Expansion microscopy of C. elegans

Author

Yu, Chih-Chieh (Jay), primary, Barry, Nicholas C, additional, Wassie, Asmamaw T, additional, Sinha, Anubhav, additional, Bhattacharya, Abhishek, additional, Asano, Shoh, additional, Zhang, Chi, additional, Chen, Fei, additional, Hobert, Oliver, additional, Goodman, Miriam B, additional, Haspel, Gal, additional, and Boyden, Edward S, additional

Published
2020
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16. Expansion microscopy of C. elegans

Author

Gal Haspel, Abhishek Bhattacharya, Anubhav Sinha, Chih-Chieh Jay Yu, Oliver Hobert, Miriam B. Goodman, Nicholas C Barry, Fei Chen, Edward S. Boyden, Shoh Asano, Chi Zhang, Asmamaw T Wassie, Yu, Chih-Chieh Jay [0000-0001-8713-0446], Hobert, Oliver [0000-0002-7634-2854], Goodman, Miriam B [0000-0002-5810-1272], Haspel, Gal [0000-0001-6701-697X], Boyden, Edward S [0000-0002-0419-3351], and Apollo - University of Cambridge Repository

Subjects
Tissue Fixation, Anatomical structures, Fluorescent Antibody Technique, Cell junction, Connexins, Animals, Genetically Modified, 0302 clinical medicine, Gene expression, Microscopy, Nanotechnology, Biology (General), Neurons, 0303 health sciences, Chemistry, General Neuroscience, Resolution (electron density), General Medicine, Fluorescence, humanities, Tools and Resources, immunohistochemistry, C. elegans, Medicine, expansion microscopy, QH301-705.5, Science, education, In situ hybridization, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, 030304 developmental biology, FOS: Nanotechnology, General Immunology and Microbiology, RNA, DNA, Luminescent Proteins, Microscopy, Fluorescence, Synapses, gene expression, Biophysics, in situ hybridization, super-resolution imaging, 030217 neurology & neurosurgery, Developmental Biology, Neuroscience
Abstract

Funder: John Doerr, Funder: The Open Philanthropy Project, Funder: Lisa Yang, We recently developed expansion microscopy (ExM), which achieves nanoscale-precise imaging of specimens at ~70 nm resolution (with ~4.5x linear expansion) by isotropic swelling of chemically processed, hydrogel-embedded tissue. ExM of C. elegans is challenged by its cuticle, which is stiff and impermeable to antibodies. Here we present a strategy, expansion of C. elegans (ExCel), to expand fixed, intact C. elegans. ExCel enables simultaneous readout of fluorescent proteins, RNA, DNA location, and anatomical structures at resolutions of ~65-75 nm (3.3-3.8x linear expansion). We also developed epitope-preserving ExCel, which enables imaging of endogenous proteins stained by antibodies, and iterative ExCel, which enables imaging of fluorescent proteins after 20x linear expansion. We demonstrate the utility of the ExCel toolbox for mapping synaptic proteins, for identifying previously unreported proteins at cell junctions, and for gene expression analysis in multiple individual neurons of the same animal.

Published
2020

17. ExCel: Super-Resolution Imaging of C. elegans with Expansion Microscopy.

Author

Yu CJ, Orozco Cosio DM, and Boyden ES

Subjects
Animals, DNA, Microscopy, Fluorescence methods, RNA, Caenorhabditis elegans, Proteins
Abstract

Studies of C. elegans will benefit from a powerful method for super-resolution imaging of proteins and mRNAs at any 3-D locations throughout the entire animal. Conventional methods of super-resolution imaging in C. elegans, such as STORM, PALM, SR-SIM and STED, are limited by imaging depths that are insufficient to map the entire depth of adult worms, and involve hardware that may not be accessible to all labs. We recently developed expansion of C. elegans (ExCel), a method for physically magnifying fixed whole animals of C. elegans with high isotropy, which provides effective resolutions finer than the diffraction limit, across the entire animal, on conventional confocal microscopes. In this chapter, we present a family of three detailed ExCel protocols. The standard ExCel protocol features simultaneous readout of diverse molecules (fluorescent proteins, RNA, DNA, and general anatomy), all at ~70 nm resolution (~3.5× linear expansion). The epitope-preserving ExCel protocol enables imaging of endogenous proteins with off-the-shelf antibodies, at a ~ 100 nm resolution (~2.8× linear expansion). The iterative ExCel protocol allows readout of fluorescent proteins at ~25 nm resolution (~20× linear expansion). The protocols described here comprise a versatile toolbox for super-resolution imaging of C. elegans., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2022
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18. Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems.

Author

Alon S, Goodwin DR, Sinha A, Wassie AT, Chen F, Daugharthy ER, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao CC, Suk HJ, Wang R, Yu CJ, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A, Church GM, Marblestone AH, and Boyden ES

Subjects
Animals, Breast Neoplasms immunology, Breast Neoplasms pathology, Dendritic Spines, Female, Humans, Mice, Visual Cortex, Gene Expression Profiling methods, Molecular Imaging methods, Sequence Analysis, RNA methods, Single-Cell Analysis methods
Abstract

Methods for highly multiplexed RNA imaging are limited in spatial resolution and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to the mouse brain, which yielded the readout of thousands of genes, including splice variants. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in the neurons of the mouse hippocampus, revealing patterns across multiple cell types, layer-specific cell types across the mouse visual cortex, and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus, ExSeq enables highly multiplexed mapping of RNAs from nanoscale to system scale., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Published
2021
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