FOODOMICS DATABASE: A NEW TOOL FOR ESTIMATING MOLECULAR PROFILES IN NUTRIENTS INTAKE DURING PRECISION KETOGENIC THERAPY By LUJIA YANG A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2018 © 2018 Lujia Yang To Haiming ACKNOWLEDGMENTS I would like to thank my mentor, Dr. Peggy Borum, for her support and guidance which helped me learn a lot through two years. I would like to thank all my committee members, Dr. Anne Mathews, Dr. Amarat Simonne and Dr. Daniel Maxwell, for their support and contribution to my project. I would like to thank Jurate Lukosaityte for her support to my work. I would like to thank undergraduate students, Alexa and Shreya for their contribution to my work. Lastly, I would like to thank my parents and my best friend, Haiming Ye, for their continued love. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 8 LIST OF FIGURES .......................................................................................................... 9 LIST OF ABBREVIATIONS ........................................................................................... 14 ABSTRACT ................................................................................................................... 15 CHAPTER 1 INTRODUCTION .................................................................................................... 17 Diet Therapy ........................................................................................................... 17 Precision Ketogenic Therapy .................................................................................. 18 Data Collections Methods for Dietary Intake ........................................................... 21 Molecular Compounds Associated with Seizure Responses .................................. 22 USDA SR 28 Database........................................................................................... 25 Hypothesis .............................................................................................................. 26 2 CREATION OF FOODOMICS DATABASE ............................................................ 27 Background ............................................................................................................. 27 Methods .................................................................................................................. 27 Nutrition Facts Label Database ........................................................................ 27 The structure of NFL database .................................................................. 28 NFL data collection .................................................................................... 29 NFL data entering and auditing .................................................................. 29 Create Foodomics Database ............................................................................ 30 Observations from USDA SR 28 ................................................................ 30 The assumptions based on USDA SR 28 .................................................. 31 The purpose of using USDA SR 28 database to create foodomics database ................................................................................................. 31 Molecular profile of individual USDA foods database ................................ 31 Molecular profile of USDA composite generic foods database .................. 32 Foodomics Database ....................................................................................... 33 Foodomics Database Results ................................................................................. 34 Discussion .............................................................................................................. 38 Conclusion .............................................................................................................. 40 3 APPLICATION OF FOODOMCIS DATABASE TO TWO PATIENTS ..................... 68 Background ............................................................................................................. 68 5 Methods .................................................................................................................. 68 Study Design .................................................................................................... 68 PKT Recipe ...................................................................................................... 70 Daily Intake Records ........................................................................................ 70 Subjects............................................................................................................ 71 Classification of Macronutrients ........................................................................ 71 Classification of amino acids ...................................................................... 72 Classification of fatty acids ......................................................................... 73 Classification of carbohydrates .................................................................. 75 Statistics ................................................................................................................. 75 Results .................................................................................................................... 75 Can the Foodomics Database Document the PKT Ratio and Macronutrients Intake Over Time on PKT? ............................................................................ 75 Can the Foodomics Database Document Intake of Each Amino Acid, Fatty Acid, and Individual Carbohydrate Over Time on PKT? ................................ 76 Can the Foodomics Database Document the Intake of EAA Over Time on PKT? ............................................................................................................. 77 Can the Foodomics Database Show the Relationship of Each Amino Acid to Other Individual Amino Acids? ...................................................................... 78 Can the Foodomics Database Document Saturated Fatty Acids Profile/ Monounsaturated Fatty Acids Profile/ Polyunsaturated Fatty Acids Profile of Intake Over Time? ..................................................................................... 78 Can the Foodomics Database Document the Daily Omega-6 to Omega-3 Ratio of Intake Over Time? ........................................................................... 81 Can the Foodomics Database Document the Difference Between Using the Net Carbohydrates Calculation Method and PKT Carbohydrate Calculation Method? ..................................................................................... 82 Discussion .............................................................................................................. 83 Conclusion .............................................................................................................. 85 4 SUMMARY ........................................................................................................... 140 APPENDIX A DOCUMENTATION FOR CREATING THE MOLECULAR PROFILE OF INDIVIDUAL USDA FOODS DATABASE ............................................................. 142 B DOCUMENTATION FOR CREATING MOLECULAR PROFILE OF USDA COMPOSITE GENERIC FOODS DATABASE ..................................................... 147 Single Composite Generic Food Database ........................................................... 147 Mixed Composite Generic Food Database ........................................................... 150 Molecular Profile of USDA Composite Generic Foods database .......................... 151 C DOCUMENTATION FOR CUTTING 30 NUTRIENTS FROM MOLECULAR PROFILE OF INDIVIDUAL USDA FOODS DATABASE ....................................... 158 6 D FOODOMICS NUTRIENTS LIST .......................................................................... 161 E SUPPLEMENTAL TABLE OF NUMBERS OF COMPOSITE GENERIC FOOD IN DIFFERENT FOOD CATEGORIES ................................................................. 164 F SUPPLEMENTAL TABLE OF FOODOMICS DATABASE DICTIONARY ............. 165 G SUPPLEMENTAL FIGURE OF NUTRITION FACTS LABEL OF “ROSS CARBOHYDRATE FREE” PRODUCT.................................................................. 178 LIST OF REFERENCES ............................................................................................. 179 BIOGRAPHICAL SKETCH .......................................................................................... 187 7 LIST OF TABLES Table page 2-1 Table of summary of five database ..................................................................... 41 2-2 Table of summary of molecular profile of USDA composite generic foods database ............................................................................................................. 42 3-1 Data quality number ........................................................................................... 86 3-2 Day quality number ............................................................................................. 87 3-3 Demographic of two patients ............................................................................. 88 3-4 Classification of amino acids .............................................................................