@article{f4a6f886ce5e4cc2870bc8548d9a876f,
title = "Proteomics in the chicken: Tools for understanding immune responses to avian diseases",
abstract = "The entire chicken genome sequence will be available by the time this review is in press. Chickens will be the first production animal species to enter the {"}postgenomic era.{"} This fundamental structural genomics achievement allows, for the first time, complete functional genomics approaches for understanding the molecular basis of chicken normo- and pathophysiology. The functional genomics paradigm, which contrasts with classical functional genetic investigations of one gene (or few) in isolation, is the systematic holistic genetic analyses of biological systems in defined contexts. Context-dependent gene interactions are the fundamental mechanics of all life. Functional genomics uses high-throughput large-scale experimental methods combined with statistical and computational analyses. Projects with expressed sequence tags in chickens have already allowed the creation of cDNA microarrays for large-scale context-dependant mRNA analysis (transcriptomics). However, proteins are the functional units of almost all biological processes, and protein expression very often bears no correlation to mRNA expression. Proteomics, a discipline within functional genomics, is the context-defined analysis of complete complements of proteins. Proteomics bridges the ~{"}sequence-to-phenotype gap;{"} it complements structural and other functional genomics approaches. Proteomics requires high capital investment but has ubiquitous biological applications. Although currently the fastest-growing human biomedical discipline, new paradigms may need to be established for production animal proteomics research. The prospective promise and potential pitfalls of using proteomics approaches to improve poultry pathogen control will be specifically highlighted. The first stage of our recently established proteomics program is global protein profiling to identify differentially expressed proteins in the context of the commercially important pathogens. Our trials and tribulations in establishing our proteomics program, as well some of our initial data to understand chicken immune system function, will be discussed.",
keywords = "Mass spectrometry, Polyacrylamide gel electrophoresis, Proteome, Proteomic, Two-dimensional",
author = "Burgess, {S. C.}",
note = "Funding Information: with a particular emphasis on proteomics. In 2001, the MSU Life Sciences and Biotechnology Institute (LSBI) was established and funded to be a core facility with proteomics equipment, training, and seed funding. The Mississippi Functional Genomics Network was established and funded by the National Institutes of Health (NIH). The State of Mississippi is heavily reliant on agriculture for its income, and the poultry industry is the primary income earner. MSU strongly supports Mississippi{\textquoteright}s agriculture industries, and one of the missions of the CVM is to develop an internationally recognized poultry research program. At the same time, rumors of NIH funding the sequencing of the chicken genome were circulating. My personal background was in genetic resistance to poultry disease. Proteomics in the chicken was a natural fit. Funding Information: Not all immune responses and immune and nonimmune cell interactions are beneficial. Immunopathologies are important causes of disease. Proteome mapping has implicated IFN-γ, IL-1, and IL-6 in the pathogenesis of inflammatory bowel disease (Barcelo-Batllori et al., 2002) and IFN-γ in human skin aging (Gromov et al., 2003). The deleterious effects of IL-1β on islets of Langerhans in a rat model of diabetes were mapped at a proteomic level, including identifying changes in PTM (Larsen et al., 2001). During work aimed at identifying the mechanisms underlying cancer metastasis, a potential role for IL-18 was suggested (Jiang et al., 2003). IL-18 was present in a highly metastatic cell line but absent in a poorly metastatic cell line. Both cell lines were derived from the same parental cell line. The association of IL-18 with metastasis was supported by IL-18 sense/IL-18 antisense experiments. Funding Information: Much of what is in this review was learned at the inaugural proteomics course at CSHL (New York, November 2002). I am grateful to have been in the company of the other 15 students from around the world on that 15-d (and night!) course. I am indebted to the instructors P. Andrews (University of Michigan), A. Link (Vanderbilt University), and J. LaBaer (Harvard University); the teaching assistants P. Braun (Harvard University), S. Vazquez (University of Michigan), and J. Jennings (Vanderbilt University); and all of the visiting instructors for catapulting me into the proteomics world. I am also thankful to J. McPherson (Washington University), M. Karpuj (UCSD), and S. Zhang (Columbia University) who were my lab group paddrtners and were both inspirational and educational in many ways. My entry into proteomics has been facilitated by the CVM and the LSBI at MSU. I thank particularly A. Wood and T. Pechan (MSU) for helpful discussion and also the former for paying for me to attend the CSHL proteomics course. I thank A. Shack (MSU) who has worked extremely hard to perfect 2-D PAGE; we are extremely collaborative. In the 18 mo that I have been at MSU, a number of collaborations have evolved. Some of that data shown and mentioned are a result of these collaborations. The following people are collaborators who have material in this review or have contributed specific suggestions for poultry immu-noproteomics: B. Gao (MSU), L. Hansen (MSU), B. Holmes (MSU), M. Kidd (MSU), M. Lawrence (MSU), M. Parcells (University of Arkansas), T. Pharr (MSU), and C. Weaver (MSU). Finally, I thank J. Ainsworth, J. Burgess, D. McGee, and M. Lawrence (MSU) for editorial input. This work has been supported by seed grants from MSU, CVM, and LSBI and by the USDA. MAFES journal number J10381.",
year = "2004",
month = apr,
doi = "10.1093/ps/83.4.552",
language = "English (US)",
volume = "83",
pages = "552--573",
journal = "Poultry science",
issn = "0032-5791",
publisher = "Elsevier Inc.",
number = "4",
}