Semester

Spring

Date of Graduation

2014

Document Type

Dissertation

Degree Type

PhD

College

Eberly College of Arts and Sciences

Department

Biochemistry

Committee Chair

Jonathan W. Boyd

Committee Co-Chair

Lisa A. Holland

Committee Member

Fred L. King

Committee Member

Justin Legleiter

Committee Member

James P. O'Callaghan

Abstract

Cellular signaling is a complex system of biological communication that coordinates cellular activities via biochemical reactions. The passing of an extracellular signal across a cell membrane to intracellular signaling molecules is referred to as signal transduction. Signals transduced across a cell's membrane influence its function, and allow the cell to respond to its local environment. Within the cell, proteins are key responders to, and carriers of, the transduced signal. A class of proteins called kinases mediate most of the signal transduction in eukaryotic cells by catalyzing the phosphorylation of substrate proteins. The post-translational modification of proteins by phosphorylation regulates protein conformation, thereby influencing its function and many cellular processes. The multitude of interactions occurring between proteins within a cell form a complex signaling network that regulates and coordinates essentially all cellular activities, where reversible phosphorylation serves as a key means by which proteins can adjust the activity of other proteins. Understanding cellular signaling is a major challenge facing scientists today. The ability to decipher the complexity of cell signaling is necessary to thoroughly understand normal biological functions, the pathophysiology of diseases, and the effects of toxic exposures. A more intimate understanding of cellular signaling could facilitate the development of improved therapeutic strategies for many diseases and conditions. Advances in technology have facilitated the collection of large datasets describing cell signal transduction networks, but it is a challenge to integrate data describing many individual proteins into concise and meaningful biological knowledge. A complete understanding of cell signaling requires the ability to capture and integrate information pertaining to as much of the entire biological network as possible. This dissertation focuses on the development and application of an approach suitable for analyzing and interpreting the networked responses of cells and tissues to stress by monitoring the phosphorylation and upregulation of proteins. The approach utilized is grounded in the field of graph theory, and describes networked stress responses based solely on experimental condition-specific data. The approach's ability to describe the mode of action for an unknown toxic exposure in vitro is demonstrated. The approach is also utilized to depict low dose toxicant induced perturbations in the balance between mitogen activated protein kinase signaling pathways in vitro, providing an informative and sensitive means of assessing toxicological effects on biological systems. Finally, the analysis is used to investigate the complex networked response of muscle tissue to traumatic injury.

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