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The Functional Profiles of Chicken Eggs Incubated Under THE FUNCTIONAL PROFILES OF CHICKEN EGGS INCUBATED UNDER MONOCHROMATIC LIGHTING A Dissertation by MOHAMED MAGDY ABDELFATTAH IBRAHIM Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Giridhar Athrey Committee Members, John B. Carey Luc R. Berghman Gregory S. Archer Head of Department, Audrey McElroy May 2021 Major Subject: Poultry Science Copyright 2021 Mohamed Magdy Abdelfattah Ibrahim ABSTRACT Poultry production remains susceptible to significant infectious disease threats such as Avian Flu, and Newcastle Disease Virus (NDV), which threaten the supply of poultry production. My dissertation research addresses this challenge by leveraging avian circadian biology to improve responses to vaccines to enhance poultry performance. The central hypothesis is that specific visible light wavelengths would enhance circadian rhythm development in ovo, leading to improved immune responses. I addressed an essential question regarding the effect of providing photoperiods with different wavelengths (Blue, Green, and White) on circadian rhythm development and its interplay with the immune response following the NDV challenge in chick embryos using the RNAseq technology. Our results showed that incubating chicken embryos under blue light 450nm was most efficient in entraining the circadian rhythm in lung tissue, compared to white light or dark treatment. Blue light showed a specific impact on skeletal muscle, regulation of striated muscle contraction, Glycerolipid metabolism, and development of neurons. The white light incubation led to a photo-acceleration stimulant effect on epidermal growth factor receptor signaling pathway, ErbB signaling pathway, MAPK signaling pathway, and Insulin signaling pathway were upregulated in white light non-challenged treatment. The response to NDV challenging showed a distinct transcriptome profile between blue and white light. The blue light showed a potent innate immune response, targeting viral replication, clearly pointing to antiviral response. ii The white light showed less immune response, but more pronounced cell proliferation and metabolic state, suggesting photo-acceleration as the primary process, particularly T cell development, T cell homeostasis, and T lymphocytes' quantity, suggests a rapid or ongoing transition between innate and adaptive immunity. This observation paves the way to photo-accelerated effect of providing white light during chicken egg incubation on organismal development and immune response. It is noteworthy that unvaccinated white light incubated chicks hatched 6-8 h earlier than other blue or dark incubation at the organism level. In conclusion, this study is the first to generated high-resolution RNASeq evidence demonstrating the effect of lighting color background on the circadian rhythm development and modulation of the innate immune response of chicks’ embryos challenged with NDV. iii DEDICATION This dissertation is dedicated to my family, who have been a constant support and encouragement source during the challenges of achieving my degree and life. A special feeling of gratitude to my loving parents. My late father, Magdy Ibrahim, who gifted me the ingenuity of his hand, unfortunately, did not stay in this world long enough to see his son achieved his PhD degree. My mother, Naima El-Desoky, and Grandmother Al-Sayeda Hussain, whose words of encouragement and push for tenacity ring in my ears. My brothers, Abdelfattah, Mostafa, Mahmoud, and Ahmed Ibrahim have never left my side and are very special. My wife, Nouran Elmelighy, and my kids, Malak, Hamza, and Nour Ibrahim, who have all supported, encouraged, forbearance, and for being there for me throughout the entire doctorate program. I dedicate this dissertation to my advisor during my Master of Science degree, Professor Essam A. El-Gendy, for helping to develop my academic skills, making me able to face a lot of challenges throughout the entire doctorate program. I dedicate this dissertation to Dr. Mohammad R. Khattab, Assistant Research Scientist at Gastrointestinal Laboratory, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, for his guidance and support throughout the course of this research. I also dedicate this work to my many friends who have supported me throughout this PhD. I would not have been able to complete this degree without your help. You are my inspiration and my encouragement. Thank you all. iv ACKNOWLEDGEMENTS I would like to thank my committee chair, Dr. Giridhar Athrey, and my committee members, Dr. John B. Carey, Dr. Luc R. Berghman, Dr. Gregory S. Archer, Dr. Mohammad R. Khattab for their guidance and support throughout the course of this research. Thanks also go to my friends and colleagues and the Poultry Science department faculty and staff for making my time at Texas A&M University a great experience. Finally, thanks to my mother and father for their encouragement and my wife's patience and love. v CONTRIBUTORS AND FUNDING SOURCES Contributors This work was supervised by a dissertation committee consisting of Professor Giridhar Athrey, and Professors John B. Carey, Gregory S. Archer of the Department of Poultry Science, and Professor Luc R. Berghman of the Department of Veterinary Pathobiology. Professor Giridhar Athrey assisted in the data analysis for “Chapter II and III.” All Athrey Lab members assisted in project management and dissections. All other work conducted for the dissertation was completed by the student independently. Funding Sources Graduate study was supported by four years scholarship awarded by the Cultural Affairs and Missions Sector, Ministry of Higher Education, Egypt. This work was also made possible in total by Athrey Lab funds during the graduation semester. No other funding source was utilized for this work. vi NOMENCLATURE °C Celsius °F Fahrenheit AANAT Arylalkylamine N-acetyltransferase Enzyme APCs Antigen Presenting Cells APR Acute Phase Response Signaling AUP Animal Use Protocol BCV Biological Coefficient Variation Bmal1 Brain, Muscle Arnt-like 1 BP Biological Process CC Cellular component CD Cluster of Differentiation CLOCK Circadian locomotor output cycles kaput DAVID Database for Annotation, Visualization, and Integrated Discovery DEGs Differentially Expressed Genes EID50 50% Embryo Infectious Dose ES Enrichment score FC Fold change FDR False Discovery Rate GO Gene ontology IACUC Institutional Animal Care and Use Committee vii IFN-ά Interferon-alpha IFN-β Interferon-beta IFN-γ Interferon-gamma IL6 Interleukin-6 IPA Ingenuity Pathway Analysis IRF Interferon Regulator Factor JAK Janus Kinase KEGG Kyoto Encyclopedia of Genes and Genomes LEDs Light Emitting Diode LPS lipopolysaccharide MAPK Mitogen-Activated Protein Kinases MF molecular function NDV Newcastle disease virus RIN RNA Integrity Number SCN Suprachiasmatic Nucleus SMART Simple Modular Architecture Research Tool STAT1 Signal transducer and activator of transcription 1 TIGSS Texas A&M Institute for Genome Sciences and Society TLR Toll-like receptor TNF Tumor necrosis factor TTFL Transcriptional/post-translational feedback loop WV Wavelength viii TABLE OF CONTENTS Page ABSTRACT .......................................................................................................................ii DEDICATION .................................................................................................................. iv ACKNOWLEDGEMENTS ............................................................................................... v CONTRIBUTORS AND FUNDING SOURCES ............................................................. vi NOMENCLATURE .........................................................................................................vii TABLE OF CONTENTS .................................................................................................. ix LIST OF FIGURES ..........................................................................................................xii LIST OF TABLES .........................................................................................................xvii CHAPTER I INTRODUCTION AND LITERATURE REVIEW .................................... 1 Introduction .................................................................................................................... 1 Literature Review ........................................................................................................... 2 Reported Effects of Photo-Biostimulation During Incubation ................................... 2 Avian Circadian System ............................................................................................. 3 Clock Genes and Circadian Rhythm Regulation ........................................................ 4 Ontogeny of Circadian Rhythm in Avian Species ..................................................... 5 Factors Affecting the Ontogeny of Circadian Rhythm in Avian Species .................. 6 Circadian Rhythms and Immune System Interplay .................................................... 7 Obstructed Circadian Rhythm and Homeostasis ........................................................ 8 Objective and Central Hypothesis .................................................................................. 9 Study Aims ..................................................................................................................... 9 CHAPTER II EFFECTS OF MONOCHROMATIC LIGHTING
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