Download the full-sized PDF of Directed Evolution Approaches for Improved Genetically Encoded Fluorescent Calcium Ion and Voltage IndicatorsDownload the full-sized PDF



Permanent link (DOI):


Export to: EndNote  |  Zotero  |  Mendeley


This file is in the following communities:

Graduate Studies and Research, Faculty of


This file is in the following collections:

Theses and Dissertations

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


Other title
Directed evolution
Fluorescent protein
Fluorescent imaging
Fluorescent indicator
Type of item
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 of Chemistry

Date accepted
Graduation date
Doctor of Philosophy
Degree level
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.
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

File Details

Date Uploaded
Date Modified
Audit Status
Audits have not yet been run on this file.
File format: pdf (Portable Document Format)
Mime type: application/pdf
File size: 17397419
Last modified: 2016:06:24 18:16:57-06:00
Filename: Zhao_Yongxin_201404_PhD.pdf
Original checksum: 512ef41f10a7c7be6cdb1f50dd976b77
Well formed: true
Valid: true
Status message: Too many fonts to report; some fonts omitted. Total fonts = 1089
File title: Yongxin Zhao
File author: Yongxin(Leon) Zhao
Page count: 293
Activity of users you follow
User Activity Date