Abstract

We developed a new method, SUT (Scheme Update on tissue Transparency), to view cardiac microstructures and unveil the molecular changes underlying cardiac diseases. SUT is an effective method to clear whole-hearts from different species. Over the course of 4 - 6 days we obtained transparent whole-layer left ventricular tissues from mice with only an approximate 1% protein loss. In addition, EAL (Electrophoretic Antibody Labeling) was used to achieve fast antibody labeling by electric force, which significantly reduced antibody incubation time from days to hours. SUT, together with EAL and modern imaging techniques, were successfully used to visualize three-dimensional spatial distribution of various molecules in cardiac tissue. We also observed changes in the number and phenotypes of fibroblasts during post-myocardial infarction in a stereoscopic pattern. We believe that our technique opens a new avenue to explore the mechanisms underlying cardiac diseases.

© 2018 Optical Society of America

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    [Crossref] [PubMed]
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2017 (1)

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
[Crossref] [PubMed]

2016 (1)

2015 (2)

D. S. Richardson and J. W. Lichtman, “Clarifying Tissue Clearing,” Cell 162(2), 246–257 (2015).
[Crossref] [PubMed]

J. R. Epp, Y. Niibori, H. L. Hsiang, V. Mercaldo, K. Deisseroth, S. A. Josselyn, and P. W. Frankland, “Optimization of CLARITY for Clearing Whole-Brain and Other Intact Organs(1,2,3),” eNeuro 2(3), 2 (2015).
[Crossref] [PubMed]

2014 (6)

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

K. Tainaka, S. I. Kubota, T. Q. Suyama, E. A. Susaki, D. Perrin, M. Ukai-Tadenuma, H. Ukai, and H. R. Ueda, “Whole-body imaging with single-cell resolution by tissue decolorization,” Cell 159(4), 911–924 (2014).
[Crossref] [PubMed]

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

R. Tomer, L. Ye, B. Hsueh, and K. Deisseroth, “Advanced CLARITY for rapid and high-resolution imaging of intact tissues,” Nat. Protoc. 9(7), 1682–1697 (2014).
[Crossref] [PubMed]

J. D. Lajiness and S. J. Conway, “Origin, development, and differentiation of cardiac fibroblasts,” J. Mol. Cell. Cardiol. 70, 2–8 (2014).
[Crossref] [PubMed]

A. V. Shinde and N. G. Frangogiannis, “Fibroblasts in myocardial infarction: a role in inflammation and repair,” J. Mol. Cell. Cardiol. 70, 74–82 (2014).
[Crossref] [PubMed]

2013 (5)

F. A. van Nieuwenhoven and N. A. Turner, “The role of cardiac fibroblasts in the transition from inflammation to fibrosis following myocardial infarction,” Vascul. Pharmacol. 58(3), 182–188 (2013).
[Crossref] [PubMed]

W. Chen and N. G. Frangogiannis, “Fibroblasts in post-infarction inflammation and cardiac repair,” Biochim. Biophys. Acta 1833(4), 945–953 (2013).
[Crossref] [PubMed]

K. Chung and K. Deisseroth, “CLARITY for mapping the nervous system,” Nat. Methods 10(6), 508–513 (2013).
[Crossref] [PubMed]

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

M. T. Ke, S. Fujimoto, and T. Imai, “SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction,” Nat. Neurosci. 16(8), 1154–1161 (2013).
[Crossref] [PubMed]

2012 (3)

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS One 7(3), e33916 (2012).
[Crossref] [PubMed]

E. P. Daskalopoulos, B. J. Janssen, and W. M. Blankesteijn, “Myofibroblasts in the infarct area: concepts and challenges,” Microsc. Microanal. 18(1), 35–49 (2012).
[Crossref] [PubMed]

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H. U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7(11), 1983–1995 (2012).
[Crossref] [PubMed]

2011 (1)

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

2010 (1)

M. Dobaczewski, C. Gonzalez-Quesada, and N. G. Frangogiannis, “The extracellular matrix as a modulator of the inflammatory and reparative response following myocardial infarction,” J. Mol. Cell. Cardiol. 48(3), 504–511 (2010).
[Crossref] [PubMed]

2009 (1)

K. E. Porter and N. A. Turner, “Cardiac fibroblasts: at the heart of myocardial remodeling,” Pharmacol. Ther. 123(2), 255–278 (2009).
[Crossref] [PubMed]

2007 (1)

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

2006 (1)

N. G. Frangogiannis, “The Mechanistic Basis of Infarct Healing,” Antioxid. Redox Signal. 8(11-12), 1907–1939 (2006).
[Crossref] [PubMed]

Abe, T.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Andalman, A. S.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Ando, R.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Becker, K.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H. U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7(11), 1983–1995 (2012).
[Crossref] [PubMed]

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS One 7(3), e33916 (2012).
[Crossref] [PubMed]

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Bernstein, H.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Blankesteijn, W. M.

E. P. Daskalopoulos, B. J. Janssen, and W. M. Blankesteijn, “Myofibroblasts in the infarct area: concepts and challenges,” Microsc. Microanal. 18(1), 35–49 (2012).
[Crossref] [PubMed]

Bocancea, D.

Bradke, F.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H. U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7(11), 1983–1995 (2012).
[Crossref] [PubMed]

Cai, L.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Chen, C. K.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Chen, W.

W. Chen and N. G. Frangogiannis, “Fibroblasts in post-infarction inflammation and cardiac repair,” Biochim. Biophys. Acta 1833(4), 945–953 (2013).
[Crossref] [PubMed]

Chung, K.

K. Chung and K. Deisseroth, “CLARITY for mapping the nervous system,” Nat. Methods 10(6), 508–513 (2013).
[Crossref] [PubMed]

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Conway, S. J.

J. D. Lajiness and S. J. Conway, “Origin, development, and differentiation of cardiac fibroblasts,” J. Mol. Cell. Cardiol. 70, 2–8 (2014).
[Crossref] [PubMed]

Daskalopoulos, E. P.

E. P. Daskalopoulos, B. J. Janssen, and W. M. Blankesteijn, “Myofibroblasts in the infarct area: concepts and challenges,” Microsc. Microanal. 18(1), 35–49 (2012).
[Crossref] [PubMed]

Davidson, T. J.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Deininger, K.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Deisseroth, K.

J. R. Epp, Y. Niibori, H. L. Hsiang, V. Mercaldo, K. Deisseroth, S. A. Josselyn, and P. W. Frankland, “Optimization of CLARITY for Clearing Whole-Brain and Other Intact Organs(1,2,3),” eNeuro 2(3), 2 (2015).
[Crossref] [PubMed]

R. Tomer, L. Ye, B. Hsueh, and K. Deisseroth, “Advanced CLARITY for rapid and high-resolution imaging of intact tissues,” Nat. Protoc. 9(7), 1682–1697 (2014).
[Crossref] [PubMed]

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

K. Chung and K. Deisseroth, “CLARITY for mapping the nervous system,” Nat. Methods 10(6), 508–513 (2013).
[Crossref] [PubMed]

Denisin, A. K.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Desco, M.

Deussing, J. M.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Deverman, B. E.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Dobaczewski, M.

M. Dobaczewski, C. Gonzalez-Quesada, and N. G. Frangogiannis, “The extracellular matrix as a modulator of the inflammatory and reparative response following myocardial infarction,” J. Mol. Cell. Cardiol. 48(3), 504–511 (2010).
[Crossref] [PubMed]

Dodt, H. U.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H. U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7(11), 1983–1995 (2012).
[Crossref] [PubMed]

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS One 7(3), e33916 (2012).
[Crossref] [PubMed]

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Eder, M.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Egen, J. G.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H. U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7(11), 1983–1995 (2012).
[Crossref] [PubMed]

Eguchi, M.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Epp, J. R.

J. R. Epp, Y. Niibori, H. L. Hsiang, V. Mercaldo, K. Deisseroth, S. A. Josselyn, and P. W. Frankland, “Optimization of CLARITY for Clearing Whole-Brain and Other Intact Organs(1,2,3),” eNeuro 2(3), 2 (2015).
[Crossref] [PubMed]

Ertürk, A.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H. U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7(11), 1983–1995 (2012).
[Crossref] [PubMed]

Frangogiannis, N. G.

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M. T. Ke, S. Fujimoto, and T. Imai, “SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction,” Nat. Neurosci. 16(8), 1154–1161 (2013).
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H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
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M. Dobaczewski, C. Gonzalez-Quesada, and N. G. Frangogiannis, “The extracellular matrix as a modulator of the inflammatory and reparative response following myocardial infarction,” J. Mol. Cell. Cardiol. 48(3), 504–511 (2010).
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K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
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Grosenick, L.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
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H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
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A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H. U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7(11), 1983–1995 (2012).
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J. R. Epp, Y. Niibori, H. L. Hsiang, V. Mercaldo, K. Deisseroth, S. A. Josselyn, and P. W. Frankland, “Optimization of CLARITY for Clearing Whole-Brain and Other Intact Organs(1,2,3),” eNeuro 2(3), 2 (2015).
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R. Tomer, L. Ye, B. Hsueh, and K. Deisseroth, “Advanced CLARITY for rapid and high-resolution imaging of intact tissues,” Nat. Protoc. 9(7), 1682–1697 (2014).
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Imai, T.

M. T. Ke, S. Fujimoto, and T. Imai, “SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction,” Nat. Neurosci. 16(8), 1154–1161 (2013).
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K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS One 7(3), e33916 (2012).
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A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H. U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7(11), 1983–1995 (2012).
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H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
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E. P. Daskalopoulos, B. J. Janssen, and W. M. Blankesteijn, “Myofibroblasts in the infarct area: concepts and challenges,” Microsc. Microanal. 18(1), 35–49 (2012).
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J. R. Epp, Y. Niibori, H. L. Hsiang, V. Mercaldo, K. Deisseroth, S. A. Josselyn, and P. W. Frankland, “Optimization of CLARITY for Clearing Whole-Brain and Other Intact Organs(1,2,3),” eNeuro 2(3), 2 (2015).
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K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
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H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
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M. T. Ke, S. Fujimoto, and T. Imai, “SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction,” Nat. Neurosci. 16(8), 1154–1161 (2013).
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K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
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E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
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E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
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Komuro, I.

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
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K. Tainaka, S. I. Kubota, T. Q. Suyama, E. A. Susaki, D. Perrin, M. Ukai-Tadenuma, H. Ukai, and H. R. Ueda, “Whole-body imaging with single-cell resolution by tissue decolorization,” Cell 159(4), 911–924 (2014).
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B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
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H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
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J. D. Lajiness and S. J. Conway, “Origin, development, and differentiation of cardiac fibroblasts,” J. Mol. Cell. Cardiol. 70, 2–8 (2014).
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Lee, J. K.

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
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Leischner, U.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
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Lichtman, J. W.

D. S. Richardson and J. W. Lichtman, “Clarifying Tissue Clearing,” Cell 162(2), 246–257 (2015).
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Lubeck, E.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
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Mattis, J.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
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Mauch, C. P.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H. U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7(11), 1983–1995 (2012).
[Crossref] [PubMed]

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Mercaldo, V.

J. R. Epp, Y. Niibori, H. L. Hsiang, V. Mercaldo, K. Deisseroth, S. A. Josselyn, and P. W. Frankland, “Optimization of CLARITY for Clearing Whole-Brain and Other Intact Organs(1,2,3),” eNeuro 2(3), 2 (2015).
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Mirzabekov, J. J.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
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Miwa, K.

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
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Miyagawa, S.

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
[Crossref] [PubMed]

Miyawaki, A.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Nakanishi, H.

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
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Nehrhoff, I.

Niibori, Y.

J. R. Epp, Y. Niibori, H. L. Hsiang, V. Mercaldo, K. Deisseroth, S. A. Josselyn, and P. W. Frankland, “Optimization of CLARITY for Clearing Whole-Brain and Other Intact Organs(1,2,3),” eNeuro 2(3), 2 (2015).
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Noda, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
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Okabe, S.

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
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Onoe, H.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
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Opthof, T.

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
[Crossref] [PubMed]

Pak, S.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Perrin, D.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

K. Tainaka, S. I. Kubota, T. Q. Suyama, E. A. Susaki, D. Perrin, M. Ukai-Tadenuma, H. Ukai, and H. R. Ueda, “Whole-body imaging with single-cell resolution by tissue decolorization,” Cell 159(4), 911–924 (2014).
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Porter, K. E.

K. E. Porter and N. A. Turner, “Cardiac fibroblasts: at the heart of myocardial remodeling,” Pharmacol. Ther. 123(2), 255–278 (2009).
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Ramakrishnan, C.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Richardson, D. S.

D. S. Richardson and J. W. Lichtman, “Clarifying Tissue Clearing,” Cell 162(2), 246–257 (2015).
[Crossref] [PubMed]

Ripoll, J.

Saghafi, S.

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS One 7(3), e33916 (2012).
[Crossref] [PubMed]

Sakata, Y.

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
[Crossref] [PubMed]

Sakaue-Sawano, A.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Sawa, Y.

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
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Schierloh, A.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Shah, S.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Sheng, M.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H. U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7(11), 1983–1995 (2012).
[Crossref] [PubMed]

Shimizu, Y.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
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Shimogori, T.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Shinde, A. V.

A. V. Shinde and N. G. Frangogiannis, “Fibroblasts in myocardial infarction: a role in inflammation and repair,” J. Mol. Cell. Cardiol. 70, 74–82 (2014).
[Crossref] [PubMed]

Susaki, E. A.

K. Tainaka, S. I. Kubota, T. Q. Suyama, E. A. Susaki, D. Perrin, M. Ukai-Tadenuma, H. Ukai, and H. R. Ueda, “Whole-body imaging with single-cell resolution by tissue decolorization,” Cell 159(4), 911–924 (2014).
[Crossref] [PubMed]

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
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Suyama, T. Q.

K. Tainaka, S. I. Kubota, T. Q. Suyama, E. A. Susaki, D. Perrin, M. Ukai-Tadenuma, H. Ukai, and H. R. Ueda, “Whole-body imaging with single-cell resolution by tissue decolorization,” Cell 159(4), 911–924 (2014).
[Crossref] [PubMed]

Tainaka, K.

K. Tainaka, S. I. Kubota, T. Q. Suyama, E. A. Susaki, D. Perrin, M. Ukai-Tadenuma, H. Ukai, and H. R. Ueda, “Whole-body imaging with single-cell resolution by tissue decolorization,” Cell 159(4), 911–924 (2014).
[Crossref] [PubMed]

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Tawara, T.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Tomer, R.

R. Tomer, L. Ye, B. Hsueh, and K. Deisseroth, “Advanced CLARITY for rapid and high-resolution imaging of intact tissues,” Nat. Protoc. 9(7), 1682–1697 (2014).
[Crossref] [PubMed]

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T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
[Crossref] [PubMed]

Treweek, J. B.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Turner, N. A.

F. A. van Nieuwenhoven and N. A. Turner, “The role of cardiac fibroblasts in the transition from inflammation to fibrosis following myocardial infarction,” Vascul. Pharmacol. 58(3), 182–188 (2013).
[Crossref] [PubMed]

K. E. Porter and N. A. Turner, “Cardiac fibroblasts: at the heart of myocardial remodeling,” Pharmacol. Ther. 123(2), 255–278 (2009).
[Crossref] [PubMed]

Ueda, H. R.

K. Tainaka, S. I. Kubota, T. Q. Suyama, E. A. Susaki, D. Perrin, M. Ukai-Tadenuma, H. Ukai, and H. R. Ueda, “Whole-body imaging with single-cell resolution by tissue decolorization,” Cell 159(4), 911–924 (2014).
[Crossref] [PubMed]

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
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K. Tainaka, S. I. Kubota, T. Q. Suyama, E. A. Susaki, D. Perrin, M. Ukai-Tadenuma, H. Ukai, and H. R. Ueda, “Whole-body imaging with single-cell resolution by tissue decolorization,” Cell 159(4), 911–924 (2014).
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K. Tainaka, S. I. Kubota, T. Q. Suyama, E. A. Susaki, D. Perrin, M. Ukai-Tadenuma, H. Ukai, and H. R. Ueda, “Whole-body imaging with single-cell resolution by tissue decolorization,” Cell 159(4), 911–924 (2014).
[Crossref] [PubMed]

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F. A. van Nieuwenhoven and N. A. Turner, “The role of cardiac fibroblasts in the transition from inflammation to fibrosis following myocardial infarction,” Vascul. Pharmacol. 58(3), 182–188 (2013).
[Crossref] [PubMed]

Vaquero, J.

Vaquero, J. J.

Wallace, J.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
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E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
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Weiler, R.

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS One 7(3), e33916 (2012).
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Yamaguchi, S.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
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B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
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T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
[Crossref] [PubMed]

Ye, L.

R. Tomer, L. Ye, B. Hsueh, and K. Deisseroth, “Advanced CLARITY for rapid and high-resolution imaging of intact tissues,” Nat. Protoc. 9(7), 1682–1697 (2014).
[Crossref] [PubMed]

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E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Yokoyama, C.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Yokoyama, T.

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
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Yoshida, A.

T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
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K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
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Zieglgänsberger, W.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
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W. Chen and N. G. Frangogiannis, “Fibroblasts in post-infarction inflammation and cardiac repair,” Biochim. Biophys. Acta 1833(4), 945–953 (2013).
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E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
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K. Tainaka, S. I. Kubota, T. Q. Suyama, E. A. Susaki, D. Perrin, M. Ukai-Tadenuma, H. Ukai, and H. R. Ueda, “Whole-body imaging with single-cell resolution by tissue decolorization,” Cell 159(4), 911–924 (2014).
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B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
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eNeuro (1)

J. R. Epp, Y. Niibori, H. L. Hsiang, V. Mercaldo, K. Deisseroth, S. A. Josselyn, and P. W. Frankland, “Optimization of CLARITY for Clearing Whole-Brain and Other Intact Organs(1,2,3),” eNeuro 2(3), 2 (2015).
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M. Dobaczewski, C. Gonzalez-Quesada, and N. G. Frangogiannis, “The extracellular matrix as a modulator of the inflammatory and reparative response following myocardial infarction,” J. Mol. Cell. Cardiol. 48(3), 504–511 (2010).
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E. P. Daskalopoulos, B. J. Janssen, and W. M. Blankesteijn, “Myofibroblasts in the infarct area: concepts and challenges,” Microsc. Microanal. 18(1), 35–49 (2012).
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Nature (1)

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
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Pharmacol. Ther. (1)

K. E. Porter and N. A. Turner, “Cardiac fibroblasts: at the heart of myocardial remodeling,” Pharmacol. Ther. 123(2), 255–278 (2009).
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K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS One 7(3), e33916 (2012).
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T. Yokoyama, J. K. Lee, K. Miwa, T. Opthof, S. Tomoyama, H. Nakanishi, A. Yoshida, H. Yasui, T. Iida, S. Miyagawa, S. Okabe, Y. Sawa, Y. Sakata, and I. Komuro, “Quantification of sympathetic hyperinnervation and denervation after myocardial infarction by three-dimensional assessment of the cardiac sympathetic network in cleared transparent murine hearts,” PLoS One 12(7), e0182072 (2017).
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F. A. van Nieuwenhoven and N. A. Turner, “The role of cardiac fibroblasts in the transition from inflammation to fibrosis following myocardial infarction,” Vascul. Pharmacol. 58(3), 182–188 (2013).
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Supplementary Material (3)

NameDescription
» Visualization 1       3D visualization of mouse whole-layer circular left ventricles. Related to Fig. 3A.
» Visualization 2       3D visualization of mouse left ventricle from endocardium to superficial myocardium. Related to Fig. 3C. The relative positions of cardiac fibers and alpha-tubulin were located with high resolution, showing that the cross striations of cardiac muscle
» Visualization 3       Layer-by-layer dynamical display of collagen I and alpha-tubulin distribution in normal mouse left ventricle. Related to Fig. 3D.

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Figures (6)

Fig. 1
Fig. 1 The equipment for electrophoretic antibody labeling. (A) The components of EAL device: 1. ice box, 2. inferior trough, 3. superior trough, 4. bracket, 5. gel container, 6. piston, 7. gel pillar, 8. sample tube, and 9. gel cap container. (B, C) Gel preparation and tissue settlement. (D) The top view of inferior and superior troughs. (E) The assembled EAL device was connected to an electrophoresis apparatus. (F) 20 μl protein ladder (Thermo Scientific) was added to the gel hole filled with PBST. Electrophoresis was run for 6 hours with constant voltage at 50 V, and electric currents at start and end were 35 mA and 13 mA, respectively.
Fig. 2
Fig. 2 Comparison of clearing effectiveness between SUT and existing clearing methods with SUT. (A) Optical transparency comparison of five primary clearing methods after 5 days clearing. Grids are 5 × 5 mm. (B-D) Comparison of clearing effects of SDS with concentration gradients (n = 6 sections per group). Statistical significance is shown for each condition versus 8% SDS (black). (E-G) Chemical screening for the best components of new clearing solution (n = 6 sections per group), with comparison of each condition versus SUT15 (black). S = 8% SDS, SUx = 8% SDS + x% Urea; SUTy = 8% SDS + 25% Urea + y% TritonX-100. (H-K) Determination of the role of each component in the new solution (n = 8 sections per group), with comparison of each condition versus S (black). S = 8% SDS, SU = 8% SDS + 25% Urea; SUT = 8% SDS + 25% Urea + 15% TritonX-100.
Fig. 3
Fig. 3 SUT cleared tissues were compatible with immunohistochemistry. Normal mouse circular whole-layer left ventricular tissues (D = 4.5 mm) passively cleared with SUT for 5 days are shown. Tissues were incubated with the primary and secondary antibody mixtures combined with DAPI. (A, B) Tissues were imaged by Zeiss light-sheet Z.1 microscopy with the ZEISS EC Plan-NEOFLUAR 5 × /0.16 objective, z = 2.0 mm. Scale bars = 500 μm. See Visualization 1. (C, D) Tissues were imaged by Leica SP8 single-photon confocal microscopy with the HC PL APO 10 × /0.40 CS and HC PL APO 40 × /1.10 W CORR CS2 objectives. zC = 117 μm. zD = 222 μm (10 × objective) and 91 μm (40 × objective). Scale bars (40 × objective) = 50 μm; scale bar (10 × objective) = 200 μm. See Visualization 1, Visualization 2 and Visualization 3.
Fig. 4
Fig. 4 SUT achieved satisfactory clearing of whole hearts of mouse, rat and pig through coronary perfusion. (A, B) Representative images of optical transparency of mouse and rat hearts before and after perfusion of SUT are shown. Scale bars = 0.5 cm. (C) Representative images of optical transparency of a pig heart before and after SUT clearing and after sRIMS perfusion are shown. Scale bars = 2 cm.
Fig. 5
Fig. 5 The quantity and phenotype of fibroblasts in the infarcted left ventricles of mice changed over time. Tissues were labeled by specific antibodies against fibroblasts, followed by imaging with Leica SP8 single-photon confocal microscopy with the HC PL APO 10 × /0.40 CS objective to show the dynamic changes in the number and phenotypes of fibroblasts and the break-down of cardiac muscles post-MI. Scale bars = 200 μm.
Fig. 6
Fig. 6 Comparison of regular shaking incubations in EAL labeled cardiac tissues. All tissues were labeled with the antibody against cardiac Troponin I followed by incubation with the second fluorescent antibody, then imaged by Leica SP8 single-photon confocal microscopy with the HC PL APO 10 × /0.40 CS and HC PL APO 40 × /1.10 W CORR CS2 objectives. The excitation light intensity of B was three times of A and C. Scale bars (40 × objective) = 50 μm; scale bars (10 × objective) = 200 μm. (A) Primary antibody: EAL was labeled for 2 hours with constant voltage at 80 V, and the start and end currents were 30 mA and 7 mA, respectively. (B) Primary antibody: shaking incubation for 3 hours at room temperature; secondary antibody: shaking incubation for 2 days at room temperature. (C) Primary antibody: shaking incubation for 2 days at room temperature; secondary antibody: shaking incubation for 2 days at room temperature.

Tables (1)

Tables Icon

Table 1 Antibodies and small-molecule dyes for immunofluorescence.

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