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Autophagy-Related (Atg) Genes in Rainbow Trout (Oncorhynchus Mykiss) and Their Role in Nutrient Restriction in Vivo and in Vitro

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Autophagy-Related (Atg) Genes in Rainbow Trout (Oncorhynchus Mykiss) and Their Role in Nutrient Restriction in Vivo and in Vitro Autophagy-related (Atg) genes in rainbow trout (Oncorhynchus mykiss) and their role in nutrient restriction in vivo and in vitro by Jaramar Balmori-Cedeño A Thesis Presented to The University of Guelph In partial fulfillment of requirements for the degree of Master of Science in Pathobiology Guelph, Ontario, Canada © Jaramar Balmori-Cedeño, September 2017 ABSTRACT Autophagy-related (Atg) genes in rainbow trout (Oncorhynchus mykiss) and their role in nutrient restriction in vivo and in vitro Jaramar Balmori-Cedeño Advisor: University of Guelph, 2017 Professor John S. Lumsden The expression of ten autophagy-related genes (ATG4, ATG5, ATG7, ATG9, ATG12, ATG13, ATG16, BECN-1, GABARAP and LC3) was examined in RTgill-W1 (gill epithelial) cells and in muscle and liver from rainbow trout (Oncorhynchus mykiss) undergoing serum nutrient restriction and compared to control groups. Six of these sequences, ATG5, ATG7, ATG9, ATG13, ATG16 and BECN-1, were previously unknown in rainbow trout. The rainbow trout sequences had highest nucleotide sequence similarity with Atlantic salmon and other fish species used for comparison in this study. In serum-restricted RTgill-W1 cells, most autophagy-related genes were significantly expressed at Day 3. In liver from feed-restricted fish, most Atg were significantly upregulated within the first 4 days. Autophagy-related gene expression in muscle was significantly upregulated between Day 8 and 15. Both tissues had a second peak of Atg upregulation at Day 21 suggesting that autophagy is maintained for longer periods of time in fish than previously understood. II ACKNOWLEDGEMENTS I would like to thank my advisor Dr. John Lumsden for his professional academic support throughout my MSc. program and for shaping my work to its best form. I would also like to express my gratitude to my committee Dr. Brandon Lillie for his guidance and contribution through the last two years. I would also like to thank Mr. R. Frank and M. Cornish from the Hagen Aqualab. None if this would be possible without your dedication. A very special thank you to Dr. Ehab Misk, Paul Huber, Leah Read and Pat Bell Rogers for teaching me all the techniques I needed, and for having the patience to answer all my doubts. Your support made this work possible. To my graduate student colleagues, Ehab Misk, Ryan Horricks, Doran Kirkbright, Juan-Ting Liu, Maureen Jarau and Paige Vroom, thank you for our talks and support when things didn’t go as planned. To Elein Hernandéz and Wendy Xiao, thank you for your friendship. A special thank you to Donna Kangas, Karla de Uslar, Marny Struyk and Cathy Bernardi, who helped me through all the administrative process and always had a smile when I needed it. I would like to thank my funding sources NSERC, the Ontario Veterinary College (OVC) and Mitacs Inc. Finally, I’d like to thank my parents and sister, who have always pushed me forward and have never let me fall, Amanda Macfarlane, for making me part of her friend-family group, and to my boyfriend, Wes Darrah, for his kind love and infinite patience. You have all helped me get to where I am. iii DECLARATION OF WORK PERFORMED All worked reported in this thesis was performed by Jaramar Balmori-Cedeño under the supervision of Dr. John Lumsden and my advisory committee Dr. Brandon Lillie, with the following exceptions: The fish trial from which the muscle and liver samples were obtained for Chapter 3 was performed by Ian Ryerse and Juan-Ting Liu. The RT-qPCR for autophagy-related genes protocols were developed by Dr. Ehab Misk and adapted and optimized by myself. The Western blot used for Chapter 2 was developed and performed by Juan-Ting Liu. The statistical analysis was done with the help of Dr. William Sears, from the Department of Population Medicine, University of Guelph. iv Table of Contents CHAPTER 1: LITERATURE REVIEW .............................................................................................1 1.1 AUTOPHAGY .....................................................................................................................1 1.1.1 Macroautophagy..................................................................................................................3 1.1.2 Microautophagy ..................................................................................................................3 1.1.3 Chaperone Mediated Autophagy.........................................................................................4 1.1.4 Autophagosome ..................................................................................................................4 1.1.5 Molecular Machinery of Autophagy ...................................................................................6 1.1.6 Core Components of Autophagy Machinery ......................................................................6 1.2 THE ROLE OF AUTOPHAGY IN NUTRIENT RESTRICTION .................................. 11 1.3 THE EFFECT OF AUTOPHAGY IN FISH DURING FEED RESTRICTION .............. 11 1.4 AUTOPHAGY IN FISH DURING INFECTIOUS DISEASE ......................................... 13 1.5 TECHNIQUES TO STUDY AUTOPHAGY ................................................................... 15 1.6 TRANSCRIPTIONAL STUDIES OF AUTOPHAGY-RELATED GENES ................... 16 RATIONALE ................................................................................................................................ 19 HYPOTHESES AND OBJECTIVES ........................................................................................... 21 CHAPTER 2: Autophagy-related (Atg) genes in rainbow trout (Oncorhynchus mykiss) and their role in nutrient restriction in RTgill-W1. ..................................................................................................... 23 2.1 ABSTRACT ............................................................................................................................ 24 2.2 INTRODUCTION .................................................................................................................. 25 2.2 MATERIAL AND METHODS .............................................................................................. 30 2.2.1 Autophagy-Related Genes Sequences in Rainbow Trout ................................................ 30 2.2.2. Primer Design ................................................................................................................. 30 2.2.3. PCR Validation and Optimization .................................................................................. 35 2.2.4. Cell Culture ..................................................................................................................... 35 2.2.5. Cell Experimental Conditions ......................................................................................... 36 2.2.6. RNA Extraction............................................................................................................... 37 2.2.7 RNA Column Purification ............................................................................................... 37 2.2.8. Reverse Transcription Polymerase Chain Reaction (RT-PCR) ...................................... 38 2.2.9. qPCR Primer Standardization ......................................................................................... 38 2.2.10. Reference Gene Validation ........................................................................................... 39 2.2.11 Western Blot Assay ........................................................................................................ 44 2.2.12 Statistical Analysis ......................................................................................................... 45 v 2.3 RESULTS ............................................................................................................................... 46 2.3.1 Autophagy-Related Gene Selection ................................................................................. 46 2.3.2. PCR Validation and qPCR Primer Assessment .............................................................. 57 2.3.3. Selection of Reference Gene(s) ....................................................................................... 71 2.3.4. Quantitative Real-Time PCR Assay................................................................................ 73 Figure 2.8. a) Western blot representing the effect of serum restriction (1%, 2%, and 10% serum percentages) on RTgill-W1 cells after incubation for 48 hours. Percentage for stacking gel was 4% and for resolving gel 15%. b) After densitometry the ratio of LC3 to β-tubulin was used to measure relative changes of LC3 expression and of expressed as means +- SD (n=2) and were analyzed with a one-way ANOVA Different letters represent significantly different values (p < 0.05). The graphs represent LC3/β-tubulin ratio.2.4 DISCUSSION ......................................................................................... 81 Chapter 3. Autophagy-related (Atg) gene expression in the liver and muscle of rainbow trout (Oncorhynchus mykiss) undergoing feed restriction ......................................................................... 87 3.1 ABSTRACT ............................................................................................................................ 88 3.2 INTRODUCTION .................................................................................................................. 89 3.3 MATERIAL AND METHODS .............................................................................................
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