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Permanent link (DOI): https://doi.org/10.7939/R39S1KR0V

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Directed Evolution Approaches for Improved Genetically Encoded Fluorescent Calcium Ion and Voltage Indicators Open Access

Descriptions

Other title
Subject/Keyword
Calcium
Directed evolution
Fluorescent protein
Voltage
Fluorescent imaging
Fluorescent indicator
Type of item
Thesis
Degree grantor
University of Alberta
Author or creator
Zhao, Yongxin
Supervisor and department
Harrison, D. Jed (Chemistry)
Campbell, Robert E. (Chemistry)
Examining committee member and department
Petersen, Nils O. (Chemistry)
Lin, Michael Z. (Pediatrics and Bioengineering at Stanford University)
Li, Liang (Chemistry)
Department
Department of Chemistry
Specialization

Date accepted
2014-05-02T09:00:10Z
Graduation date
2014-11
Degree
Doctor of Philosophy
Degree level
Doctoral
Abstract
Fluorescent proteins (FP) have revolutionized our imaging technologies and facilitated visualization of biochemical and physiological processes occurring in complex biological systems, which has opened up a new and unprecedented era in cell biology. Although FPs mainly serve as passive fluorescent labels for reporting gene expression and protein localization, FP-based indicators also serve as indispensable tools for dynamic imaging of cellular signaling including neuronal activities. However, few FP-based indicators provide robust performance for in vivo imaging, and the development of reliable FP-based indicators remains a challenging engineering problem, mainly due to lack of structural information for rational design and effective methodologies of protein engineering. The goal of this thesis work is to tackle the long-standing challenge of engineering FP-based indicators for improved performance. This thesis describes a variety of directed evolution strategies to develop FP-based indicators for neuronal activities. First, I developed a colony-based directed evolution method to screen for improved single FP-based calcium ion (Ca2+) indicators. This novel strategy accelerated the engineering of single FP-based Ca2+ indicator and led to several variants with improved performance and various new colors. This palette of new Ca2+ indicators enables simultaneous monitoring of Ca2+ transients in different cellular compartments or different types of cells, which opens up a new era of colorful Ca2+ imaging. Next, by combining microfluidic technology and colony-based screening, I designed an automated cell sorting approach that enables screening variants of FP-based Ca2+ indicator with throughput up to 300 cells/s. This new approach saved considerable time and effort for evolving a new yellow FP-based Ca2+ indicator, Y-GECO. The end product, Y-GECO1, is a useful tool for Ca2+ imaging in cell cultures and brain slices. Finally, I designed a hierarchical screening method to engineer Archaerhodopsin-based voltage indicators with a focus on improving fluorescent brightness. The latest generation of variants, designated QuasAr1 and QuasAr2, shows superior performance and brightness compared to their predecessors. Together with our collaborators, we demonstrated that QuasAr1 and QuasAr2 enable fully optical electrophysiological interrogation of neuronal circuits in intact brain tissues.
Language
English
DOI
doi:10.7939/R39S1KR0V
Rights
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
Citation for previous publication
Y. Zhao, S. Araki, J. Wu, T. Teramoto, Y-F. Chang, M. Nakano, A. S. Abdelfattah, M. Fujiwara, T. Ishihara, T. Nagai, and R. E. Campbell*, “An Expanded Palette of Genetically Encoded Ca2+ Indicators”. Science, 2011, 333, 1888-1891

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File title: Yongxin Zhao
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