Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2008 Application of Shortest-Path Network Analysis to Identify Genes that Modulate Longevity in Saccharomyces cerevisiae JR Managbanag Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Biology Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/1613 This Dissertation is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Life Sciences Virginia Commonwealth University This is to certify that the dissertation prepared by Jim Ray J. Managbanag entitled Application of Shortest-Path Network Analysis to Identify Genes that Modulate Longevity in Saccharomyces cerevisiae has been approved by his or her committee as satisfactory completion of dissertation requirement for the degree of Doctor of Philosophy (Ph.D.) in Integrative Life Sciences (ILS) Tarynn M. Witten (Chairperson), Ph.D., FGSA, Center for the Study of Biological Complexity (CSBC), School of Life Sciences, Emergency Medicine (MCV) _______________________________________________________________________ Danail G. Bonchev, Ph.D., CSBC, Department of Mathematics Lemont B. Kier, Ph.D., Department of Medicinal Chemistry Fang-Sheng Wu, Ph.D., Department of Biology Ping Xu, Ph.D., School of Dentistry Thomas F. Huff, Ph.D., Vice Provost of Life Sciences Dr. F. Douglas Boudinot, Dean of the School of Graduate Studies September 3, 2008 © Jim Ray J. Managbanag 2008 All Rights Reserved APPLICATION OF SHORTEST-PATH NETWORK ANALYSIS TO IDENTIFY GENES THAT MODULATE LONGEVITY IN SACCHAROMYCES CEREVISIAE A Dissertation submitted in partial fulfillment of the requirements for the degree Ph.D. in Integrative Life Sciences at Virginia Commonwealth University. by JIM RAY J. MANAGBANAG MS Biology, George Mason University, 2001 BA Biology, George Mason University, 1991 Director: TARYNN M. WITTEN, PH.D. ASSOCIATE PROFESSOR, CENTER FOR THE STUDY OF BIOLOGICAL COMPLEXITY, SCHOOL OF LIFE SCIENCES Virginia Commonwealth University Richmond, Virginia December 2008 Acknowledgement I am grateful to Dr. Tarynn Witten for her mentorship and for suggesting the idea for this project. Her enthusiasm, friendship and steady guidance made this endeavor very worthwhile. I would like to thank the other members of my committee: Dr. Bonchev, Dr. Kier, Dr. Wu and Dr. Xu for offering their expertise and consummate professionalism in dealing with matters pertinent to the didactic stage of my work. I am deeply indebted to Dr. Matt Kaeberlein, Dr. Brian Kennedy, Chris Murakami, Lindsey Fox, Mitsuhiro Tsuchiya, and a few other folks at the University of Washington (Seattle) for their willingness to experimentally verify the predictions made in my dissertation. I am honored to have been considered a collaborator. I would like to thank my colleagues at AmeriSci Bio-Chem for adjusting their schedules so I could attend classes during “normal” working hours. I would like to thank Mr. Barry Browder for allowing flexibility with my work schedule so I could pursue my educational goal. I would like to thank Mr. Tomi Hong for encouraging me to get a Ph.D. I would like to thank Isidro and Alicia Managbanag for leaving a good life in the Philippines so that my siblings and I could have better educational opportunities in the United States of America. Lastly, I would like to thank my wife Norma and my children Issy, Gabby, and Will for offering me their love, inspiration, and support. Table of Contents Page Acknowledgements............................................................................................................ iv List of Tables ..................................................................................................................... ix List of Figures......................................................................................................................x Chapter 1 Introduction......................................................................................................15 General Motivations....................................................................................15 Yeast as a model for aging research............................................................16 2 Overview of aging theories..............................................................................20 Reactive oxygen species (ROS): star players in multi-hit theories.............20 Program theories, genetic influences...........................................................21 Definition and characteristics of replicative aging in yeast ........................24 Fragmentation of nucleolus.........................................................................25 Changes in metabolism ...............................................................................26 Bud scar accumulation ................................................................................27 Increased size ..............................................................................................28 Loss of asymmetry ......................................................................................28 Silencing and loss of fertility.......................................................................28 3 Regulation of replicative aging in S. cerevisiae...............................................30 Caloric Restriction (CR) and the role of SIR2 ............................................30 v The TOR pathway .......................................................................................33 The role of Nicotinamide ............................................................................34 Retrograde response and the role of RTG2 .................................................35 Definition and characteristics of chronological aging in yeast ...................36 Reactive oxygen species (ROS) and chronological aging...........................38 4 Biological Networks and the study of aging....................................................41 From Euler to the present ............................................................................41 Aging and networks.....................................................................................45 5 Complexity analysis and network comparisons...............................................49 Modularity...................................................................................................49 Fragility, robustness and scaling .................................................................51 Watts-Strogatz model (small-world model) ................................................52 Motifs ..........................................................................................................53 Comparing yeast, worm and fly networks (Shannon’s information content as a metric for complexity.....................................................................54 NetworkBlast...............................................................................................55 6 Materials and Methods.....................................................................................57 Compilation of aging/longevity gene list and construction of networks.....57 Ranking the genes using vertex degree and centrality measurements ........59 Determining modularity ..............................................................................62 Determining fragility, robustness and scaling.............................................62 vi Watts and Strogatz model (small world).....................................................62 Detecting network motifs ............................................................................63 Network comparison (Determination of Shannon’s information content...63 NetworkBlast...............................................................................................63 Replicative life span experiments................................................................66 7 Results..............................................................................................................68 Replicative Network: Core (Direct Interaction)..........................................68 Construction of Composite and Binding SPLNs.........................................71 The SPLN can be further divided into modules..........................................83 The SPLN has scaling properties and is stable against random attacks......92 The SPLN conforms to “Small World” model of Watts and Strogatz........95 The SPLN shares some subgraph patterns with other complex networks ..97 Network comparison (Yeast, Fly, and Worm): application of Shannon’s information theory...............................................................................100 NetworkBlast Results................................................................................103 Replicative Assay Results: Predictive success of Binding SPLN.............105 8 Discussion......................................................................................................137 References........................................................................................................................145 Appendices.......................................................................................................................161 vii A Table of interaction types and relations