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2016 Pritchettelizab EXPLORATION OF THE CHICKEN (GALLUS GALLUS) PITUITARY GLAND TRANSCRIPTOME by Elizabeth M. Pritchett A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Animal and Food Sciences Fall 2016 © 2016 Elizabeth M. Pritchett All Rights Reserved ProQuest Number:10241042 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. ProQuest 10241042 Published by ProQuest LLC ( 2017). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code Microform Edition © ProQuest LLC. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, MI 48106 - 1346 EXPLORATION OF THE CHICKEN (GALLUS GALLUS) PITUITARY GLAND TRANSCRIPTOME by Elizabeth M. Pritchett Approved: __________________________________________________________ Limin Kung, Jr., Ph.D. Interim Chair of the Department of Animal and Food Sciences Approved: __________________________________________________________ Mark W. Rieger, Ph.D. Dean of the College of Agriculture and Natural Resources Approved: __________________________________________________________ Ann L. Ardis, Ph.D. Senior Vice Provost for Graduate and Professional Education I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Carl J. Schmidt, Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Erin M. Brannick, D.V.M. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Robert M. Dyer, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Susan J. Lamont, Ph.D. Member of dissertation committee ACKNOWLEDGMENTS This project was funded and supported by Agriculture and Food Research Initiative Competitive Grant 2011-67003-30228 from the United States Department of Agriculture National Institute of Food and Agriculture and the University of Delaware College of Agriculture and Natural Resources. I would like to express my gratitude to my advisor, Dr. Carl Schmidt for the opportunity to complete this work and for the unwavering support and advisement. I would also like to thank the members of my committee, Dr. Erin Brannick, Dr. Robert Dyer, and Dr. Susan Lamont for their guidance and support throughout this project. Special thanks to all members of the Schmidt Laboratory who helped in ways both big and small. Last, a very special thank you to my husband, Tyler and children, Logan and Katelyn. More is possible with your love and encouragement. I could not have done this without you. iv TABLE OF CONTENTS LIST OF TABLES ........................................................................................................ ix LIST OF FIGURES ....................................................................................................... xi ABSTRACT ................................................................................................................ xiv Chapter 1 INTRODUCTION .............................................................................................. 1 1.1 Heat Stress ................................................................................................. 1 1.2 Pituitary Gland........................................................................................... 5 1.2.1 Anterior Pituitary Gland ................................................................ 8 1.2.2 Pars Tuberalis ................................................................................ 9 1.2.3 Posterior Pituitary Gland ............................................................... 9 1.2.4 Anterior Pituitary Endocrine Hormones ...................................... 10 1.2.5 Pituitary Interaction with Hypothalamus and Response to Stress............................................................................................ 12 1.3 Summary.................................................................................................. 14 2 MATERIALS AND METHODS ..................................................................... 16 2.1 Experimental Design ............................................................................... 16 2.1.1 Pituitary Gland Collection Method ............................................. 19 2.1.2 Transcriptome Analysis ............................................................... 20 2.1.2.1 Differential Gene Expression Analysis ........................ 21 2.1.2.2 Relative Tissue Expression Analysis............................ 21 3 TRANSCRIPTOMIC CHANGES THROUGHOUT POST-HATCH DEVELOPMENT IN THE UNSTRESSED BROILER CHICKEN (GALLUS GALLUS) PITUITARY GLAND .................................................... 23 3.1 Abstract.................................................................................................... 23 3.2 Introduction ............................................................................................. 24 3.3 Materials and Methods ............................................................................ 25 v 3.3.1 Animal Housing and Tissue Collection ....................................... 25 3.3.2 RNA Isolation, cDNA Synthesis, RNA-seq Library Preparation, and qRT-PCR Validation ........................................ 25 3.3.3 Relative Tissue Expression Analysis........................................... 27 3.4 Results ..................................................................................................... 28 3.4.1 Enriched Genes at Day 21 and Day 22: 295 Shared Genes ........ 29 3.4.2 Enriched Genes at Day 21 (74 Genes) and Day 22 (92 Genes) .. 31 3.4.3 Enriched Genes at Day 42: 407 Genes ........................................ 31 3.4.4 Enriched Genes at Day 21, Day 22, and Day 42: 25 Shared Genes ........................................................................................... 35 3.4.5 Enriched Transcription Factor Genes .......................................... 36 3.5 Discussion................................................................................................ 39 3.5.1 Day 21 and 22: Shared and Unique Enriched Genes .................. 39 3.5.2 Day 42 Enriched Genes ............................................................... 40 3.5.3 Day 21, 22 and 42: 25 Shared Enriched Genes ........................... 43 3.5.4 Enriched Transcription Factors Genes ........................................ 44 3.6 Conclusion ............................................................................................... 46 3.7 Acknowledgements ................................................................................. 47 4 COMPARATIVE TRANSCRIPTOMICS OF BROILER CHICKENS (GALLUS GALLUS) EXPOSED TO ACUTE HEAT STRESS....................... 48 4.1 Abstract.................................................................................................... 48 4.2 Introduction ............................................................................................. 49 4.3 Materials and Methods ............................................................................ 50 4.3.1 Animal Housing and Tissue Collection ....................................... 50 4.3.2 RNA Isolation, cDNA Synthesis, and RNA-seq Library Preparation ................................................................................... 51 4.3.3 Differentially Expressed Genes (DEG) Analysis of Heat Stress versus Unstressed Pituitary Glands ............................................. 52 4.3.4 Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) Verification ............................................... 52 4.4 Results and Discussion ............................................................................ 53 4.4.1 Thermoneutral Condition DEG ................................................... 55 4.4.2 Heat Stress Condition DEG ......................................................... 56 vi 4.4.2.1 Heat Shock Proteins, Heat Responders, and Protein Folding .......................................................................... 58 4.4.2.2 Ubiquitin and Endoplasmic Reticulum-Associated Degradation .................................................................. 58 4.4.2.3 Cell Cycle and Response to Nutrient Levels ................ 61 4.4.2.4 Peptide Hormones ........................................................ 62 4.4.3 Conclusions ................................................................................
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