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Expansion Microscopy: a New Approach to Microscopic Evaluation University of South Carolina Scholar Commons Theses and Dissertations Summer 2020 Expansion Microscopy: A New Approach to Microscopic Evaluation Ashley Ferri Follow this and additional works at: https://scholarcommons.sc.edu/etd Part of the Biomedical Commons Recommended Citation Ferri, A.(2020). Expansion Microscopy: A New Approach to Microscopic Evaluation. (Master's thesis). Retrieved from https://scholarcommons.sc.edu/etd/6034 This Open Access Thesis is brought to you by Scholar Commons. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Expansion Microscopy: A New Approach to Microscopic Evaluation by Ashley Ferri Bachelor of Science University of South Carolina, 2014 Submitted in Partial Fulfillment of the Requirements For the Degree of Master of Science in Biomedical Science School of Medicine University of South Carolina 2020 Accepted by: Robert L. Price, Director of Thesis Jay D. Potts, Reader Ana Pocivavsek, Reader Cheryl L. Addy, Vice Provost and Dean of Graduate School © Copyright by Ashley Ferri, 2020 All Rights Reserved ii ACKNOWLEDGEMENTS I would like to extend thanks to my mentor Dr. Robert L. Price, and my thesis advisors Dr. Jay Potts, and Dr. Ana Pocivavsek. I would like to thank Mike Gore and Matthew Efrid of the University of South Carolina School of Medicine machine shop for their help in designing and creating a prototype for the new gelation chamber. I would also like to thank Nick Maxwell and Nathan Wagner for their help in identifying brain structures; and Lorain Junor and Anna Harper for their instruction and guidance in immunohistochemistry procedures and operation of the IRF equipment. iii ABSTRACT Optical microscopy resolution is limited by the wavelengths of light and the series of microscope lenses and other optical components used to create a magnified image of cell structures in a sample. Often the cell structures are smaller or closer together than the resolution limits of a light microscope. In 2015 the Boyden group at the Massachusetts Institute of Technology (MIT) created a sample preparation technique, expansion microscopy which involves embedding biological samples in a crosslinked, swellable, hydrogel polymer that allows for uniform physical separation of cell components so that they can subsequently be resolved by light microscopy. Using the protein retention variant of expansion microscopy, these experiments evaluated the efficacy of the technique. Forty-micron thick rat hippocampal specimens were labeled GFAP and NeuN antibodies to image the neurons and astrocytes within the tissue. The expansion process produced a 4.7-fold physical expansion of the hippocampal slices. The process was also evaluated using 50 – 100 um thick samples of mouse cardiac tissue, labeled to visualize the cytoskeleton, intercalated discs, and cellular nuclei. However, due to the strong structural integrity of cardiac tissue expansion was inconsistent and incompatible with cardiac tissue samples. Variations to the procedure are required to compensate for the rigidity and anisotropic nature of cardiac tissue. One challenge faced when expanding the samples was creation of a consistent and uniform expansion gel and handling of the fragile embedded tissue. To alleviate these difficulties, we designed a new gelation chamber that allowed for more consistent sample preparation. iv Table of Contents Acknowledgements ........................................................................................................................ iii Abstract …….. ............................................................................................................................... iv List of Tables .. .............................................................................................................................. vii List of Figures ............................................................................................................................. viii Chapter 1. Background .................................................................................................................... 1 1.1 Specific Aims ........................................................................................................................ 8 Chapter 2. Materials and Methods ................................................................................................. 10 2.1 Development of a Protocol for use in the IRF ..................................................................... 10 2.2 Examination of Intercalated Discs in Cardiac Tissue .......................................................... 15 Chapter 3. Results .......................................................................................................................... 19 3.1 Development of a Protocol for use in the IRF ..................................................................... 19 3.2 Examine the ability of Protein Retention Expansion Microscopy to evaluate cellular junctions in cardiac tissue .............................................................. 30 3.3 Design of a New Gelation Chamber .................................................................................... 33 Chapter 4. Discussion .................................................................................................................... 35 4.1 Development of a Protocol for use in the IRF ..................................................................... 35 4.2 Examine the ability of Protein Retention Expansion Microscopy to evaluate cellular junctions in cardiac tissue .............................................................. 38 4.3 Design a New Gelation Chamber ........................................................................................ 40 v References ….. .............................................................................................................................. 41 Appendix A: Protocol for use in the IRF ....................................................................................... 46 A.1. Protocol .............................................................................................................................. 46 A.2 Chemical List ..................................................................................................................... 54 A.3 Previously used fluorophores and sample types ................................................................ 56 vi List of Tables Table 1.1 Super resolution microscopy techniques ...................................................................... 2 Table A.1 Chemicals used .......................................................................................................... 47 Table A.2 Chemicals for use with Expansion Microscopy ......................................................... 54 Table A.3 Commercially available fluorophores used with expansion microscopy.................................................................................................... 56 Table A.4 Species and Tissue types previously used with expansion microscopy.................................................................................................... 60 vii List of Figures Figure 1.1. Concept and workflow of expansion microscopy techniques. (Enger, 2016) ............ 4 Figure 1.2 Expansion microscopy theory. (Asano, 2018)............................................................. 7 Figure 2.1 Coronal slice of rat brain tissue. ................................................................................ 11 Figure 2.2 Manually constructed gelation chambers as described above. ................................. 13 Figure 3.1. 20X image of rat hippocampus stained with NeuN and GFAP. ............................... 19 Figure 3.2. 40X Image of rat hippocampus stained with NeuN in green and GFAP. ................. 20 Figure 3.3. Early attempts at creating the gelation chamber with samples, gel and lid. ............. 20 Figure 3.4. Early attempts at creating the gelation chamber ...................................................... 21 Figure 3.5 Gelled sample after polymerization at 37⁰C. ............................................................. 21 Figure 3.6. Gelled removed from the gelation chamber. ............................................................ 22 Figure 3.7 Gelled sample after the surrounding gel was removed. ............................................. 22 Figure 3.8. Gelled samples in digestion buffer. .......................................................................... 22 Figure 3.9 (a) Gelled samples after overnight digestion. (b) Measurement diagram of samples pre expansion. ......................................................... 23 Figure 3.10. (a) Gelled samples after expansion. (b) Measurement diagram of expanded samples. ....................................................................................... 24 Figure 3.11. Expanded sample inside gasket. ............................................................................. 24 Figure 3.13. Screen shots of z-stack projections, post expansion. (a) screenshot of image at 20X magnification (b) screen shot of image at 40X magnification. ....................................................................................... 27 Figure 3.14. Side-by-side comparison of pre and post expansion images at 20X. (a) z-stack projection of pre expansion tissue at 20X, scale par: 20 um (b) z-stack projection of post expansion tissue
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