ii Image Processing for the Structural Analysis of Respiratory Syncytial Virus by Cryo- Electron Tomography Open Access

Abstract

iv
Abstract
Image Processing for the Structural Analysis of Respiratory Syncytial Virus
Electron Tomography
Respiratory Syncytial Virus (RSV) is a member of the Paramyxoviridae family of viruses.
RSV contains a single-stranded, negative sense RNA genome, which is encapsidated by
the viral nucleocapsid, phosphoprotein, and RNA-dependent RNA polymerase. The four
macromolecules combined form the helical ribonucleoprotein (RNP) complex. It is the
RNP that must be transferred from an infected cell to a new cell in order for the infection
process to continue.
In this study, cryo-electron tomography (cryo-ET) was used to characterize the three-
dimensional (3D) structure of purified RSV virions. The RNP was resolved as hollow
tubes with helical spokes of an approximately 9nm width in X-Y cross-sections. A
module, TubeTracker, was developed for the Amira software programs in order to
objectively map the trajectory of RNP through the 3D volumes of the RSV virions.
Several denoising algorithms were generated to improve the signal to noise ratio of the
3D data to increase the likelihood of accurate feature tracking.
Model toroids representing hollow tubular trajectories were first developed to assess the
functionality of TubeTracker under each of its programmed conditions. The model
toroids were tracked successfully under both the ideal noise-free situation as well as with
the addition of increasing amounts of white, speckle noise to the model toroid volumes.
During the application of TubeTracker to the RSV tomograms, the program performed
for several iterations, then trajectory tracking was prone to error. The failure of the
TubeTracker to function with the cryo-ET data of RSV was possibly due to poor feature
cross-correlation due to missing-wedge effects, angular search range and increments, or
limited voxel intensity ranges.

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Image Processing for the Structural Analysis of Respiratory Syncytial Virus
Electron Tomography
B.S., Georgia Institute of Technology, 2005
Advisor: Elizabeth Wright, Doctor of Philosophy
A thesis submitted to the Faculty of the
James T. Laney School of Graduate Studies of Emory University
in partial fulfillment of the requirements for the degree of
Master of Science
in
Graduate Division of Biological and Biomedical Science
Microbiology and Molecular Genetics
2012

Table of Contents

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TABLE OF CONTENTS
Distribution Agreement
i
Approval Form
ii
Abstract Cover Page
iii
Abstract
iv
Thesis Cover Page
v
Acknowledgements
vi
List of Figures
viii
List of Abbreviations
ix
List of Tables
x
CHAPTER I - INTRODUCTION
1
CHAPTER II - MATERIALS AND METHODS
14
CHAPTER III - RESULTS
18
CHAPTER IV - DISCUSSION
40
REFERENCES
45

About this Master's Thesis

Rights statement

• Permission granted by the author to include this thesis or dissertation in this repository. All rights reserved by the author. Please contact the author for information regarding the reproduction and use of this thesis or dissertation.

School	Laney Graduate School
Department	Biological and Biomedical Sciences
Subfield / Discipline	Microbiology & Molecular Genetics
Degree	MS
Submission	Master's Thesis
Language	English
Research Field	Computer Science Biology, Virology Biology, Microbiology
Keyword	Cross-correlation Respiratory Syncytial Virus Tomography Image Processing Cryo-electron
Committee Chair / Thesis Advisor	Wright, Elizabeth R., Emory University
Committee Members	Schinazi, Raymond F, Emory University Grakoui, Arash, Emory University Nagy, James, Emory University Conn, Graeme L, Emory University

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