Burgess S C
Department of Basic Sciences, Mississippi State University, College of Veterinary Medicine, PO Box 6100, Mississippi State, Mississippi 39762-6100, USA.
Poult Sci. 2004 Apr;83(4):552-73. doi: 10.1093/ps/83.4.552.
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.
在本综述付梓之时，完整的鸡基因组序列将可获取。鸡将成为首个进入“后基因组时代”的养殖动物物种。这一基础结构基因组学成就首次使得通过完整的功能基因组学方法来理解鸡正常生理和病理生理的分子基础成为可能。功能基因组学范式与孤立地对单个（或少数）基因进行经典功能遗传学研究形成对比，它是在特定背景下对生物系统进行系统的整体遗传学分析。依赖背景的基因相互作用是所有生命的基本机制。功能基因组学使用高通量大规模实验方法并结合统计和计算分析。鸡的表达序列标签项目已经使得能够创建用于大规模依赖背景的mRNA分析（转录组学）的cDNA微阵列。然而，蛋白质是几乎所有生物过程的功能单元，并且蛋白质表达常常与mRNA表达无关。蛋白质组学是功能基因组学中的一个学科，是对蛋白质完整互补物进行背景定义的分析。蛋白质组学弥合了“序列到表型的差距”；它补充了结构和其他功能基因组学方法。蛋白质组学需要大量资金投入，但具有广泛的生物学应用。尽管目前它是人类生物医学领域发展最快的学科，但可能需要为养殖动物蛋白质组学研究建立新的范式。将特别强调使用蛋白质组学方法改善家禽病原体控制的预期前景和潜在陷阱。我们最近建立的蛋白质组学计划的第一阶段是全局蛋白质谱分析，以鉴定在商业上重要的病原体背景下差异表达的蛋白质。我们在建立蛋白质组学计划过程中的试验和磨难，以及一些用于理解鸡免疫系统功能的初步数据将被讨论。
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