Acquisition of Equipment for Genomics Research

项目摘要：一项基金已被授予博士。Revie和Marcey在加州路德大学购买设备进行结构和功能基因组学研究。该项目将达到四个目标。首先，该设备将用于更快地测序古细菌嗜酸热原体122-1B2菌株的基因组。古细菌是一组微生物，它构成了生命的第三个分支，不同于其他两个分支：(1)细菌和(2)真核生物，真核生物包括酵母和多细胞生物。确定嗜酸乳杆菌基因组中的碱基序列将允许鉴定与呼吸有关的蛋白质。其次，Marcey博士将使用该设备研究果蝇（Drosophila melanogaster）体内一种与细胞信号有关的蛋白质。第三，这些设备将允许学生在正式的实验课上进行更广泛的研究项目。例如，基因组学研究将在遗传学、分子生物学、发育生物学和重组DNA技术方面进行。第四，该设备将允许生物学和生物化学的学生参与教师指导的结构和功能基因组学的研究经验。嗜酸T.古细菌可以在正常氧浓度下、极低氧浓度下或在硫存在下厌氧生长。这种生物在pH值1.7和59摄氏度的环境下生长最佳，但有趣的是，它没有细胞壁。虽然它可以减少硫，但对这个过程知之甚少。人们对这种生物如何在极低氧条件下生存的了解就更少了。考虑到嗜酸乳杆菌生长的恶劣和极端环境，这种呼吸的灵活性是相当显著的，使得对其呼吸蛋白的研究成为古细菌整体研究的一个有趣和重要的部分。为了发现和研究呼吸蛋白，该设备将更快地确定DNA中的整个碱基序列。这主要是通过对已克隆到质粒中的嗜酸乳杆菌DNA进行测序，然后将得到的片段组装成一条连续的染色体来完成的。然后对DNA进行分析，以确定生物体中基因的整体补体。一种名为Dpez的基因编码一种参与细胞通讯的新型蛋白质，即FERM结构域蛋白酪氨酸磷酸酶（PTPs），将在模式生物黑胃果蝇中进行研究。该基金资助的设备将用于确定编码与Dpez相互作用的蛋白质的基因的DNA序列。此外，还将确定产生Dpez蛋白突变形式的基因的DNA序列。将研究DPez表达的时空模式。古生菌是一种独特的有机体。包括嗜酸乳杆菌在内的许多细菌都生活在高温和低ph等极端环境中。该项目将有助于研究使细菌在极端条件下生长的蛋白质。此外，嗜酸乳杆菌在各种呼吸条件下生长的能力使得对这些蛋白质的研究更加有趣。确定生物体的整个碱基序列也将允许在嗜酸乳杆菌和其他微生物之间进行比较，这将增加对进化过程的了解。蛋白酪氨酸激酶（PTKs）和蛋白酪氨酸磷酸酶（PTPs）的相反作用之间的平衡可以调节细胞的增殖、分化和形态。PTPs已经从多种生物体中大量克隆，并且靶向亚细胞位置并与特定的信号通路相关。Dpez蛋白是第一个被描述的无脊椎FERM-PTP蛋白。对DPez的功能进行研究的目的是利用果蝇的易处理遗传学来发现这种蛋白质在模式昆虫的发育和细胞生理学中的作用。

Project AbstractA grant has been awarded to Drs. Revie and Marcey at California Lutheran University to purchase equipment to perform structural and functional genomics research. The project will meet four goals. First, the equipment will be used to more quickly sequence the genome of strain 122-1B2 of the archaeon Thermoplasma acidophilum. Archaea are a group of microorganisms that comprise a third branch of life, which are distinct from the other two branches: (1) bacteria and (2) eukaryotes, a group that includes yeast and multicellular organisms. Determining the sequence of bases in the genome of T. acidophilum will allow for the identification of proteins that are involved in respiration. Second, the equipment will be used by Dr. Marcey to study a protein involved in cellular signaling in the fruit fly Drosophila melanogaster. Third, the equipment will allow students to perform a wider variety of research projects in formal laboratory classes. For example, genomics research will be conducted in Genetics, Molecular Biology, Developmental Biology, and Recombinant DNA Techniques. Fourth, the equipment will allow Biology and Biochemistry students to engage in faculty-mentored research experiences in structural and functional genomics.The archaeon T. acidophilum can grow either aerobically under normal oxygen concentrations, under very low oxygen concentrations, or anaerobically in the presence of sulfur. The organism grows optimally at pH 1.7 and 59 degrees C, but interestingly, lacks a cell wall. Although it can reduce sulfur, little is known about this process. Even less is known about how the organism survives under very low oxygen conditions. Considering the hostile and extreme environment where T. acidophilum thrives, this flexibility of respiration is quite remarkable, making the study of its respiratory proteins an interesting and important part of the overall study of Archaea. In order to find and study the respiratory proteins, the equipment will more quickly determine the entire sequence of bases in the DNA. This will primarily be done by sequencing T. acidophilum DNA that has been cloned into a plasmid, then assembling the resulting pieces into one contiguous chromosome. The DNA will then be analyzed to determine the entire complement of genes in the organism. A gene, Dpez, that encodes a member of novel class of proteins involved in cellular communication, the FERM domain Protein Tyrosine Phosphatases (PTPs), will be studied in the model organism Drosophila melanogaster. Equipment funded by this grant will be used to determine the DNA sequences of genes encoding proteins that interact with Dpez. Also, the DNA sequences of genes that produce mutant forms of the Dpez protein will be determined. Spatial and temporal patterns of DPez expression will be investigated.Archaea are a distinct group of organisms. Many of them, including T. acidophilum, live in extreme environments such as high temperatures and low pH. This project will aid the study of proteins that enable the organism to thrive under the extreme conditions in which it grows. In addition, the ability of T. acidophilum to grow under a variety of respiratory conditions makes the study of these proteins even more interesting. Determining the entire sequence of bases in the organism will also allow for comparisons between T. acidophilum and other microorganisms that will increase knowledge of evolutionary processes. The balance between the opposite actions of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) can regulate cell proliferation, differentiation, and morphology. PTPs have been cloned in large numbers from a variety of organisms and are targeted to subcellular locations and linked to specific signaling pathways. The Dpez protein is the first invertebrate FERM-PTP described. Investigations of the functions of DPez will be conducted with the goal of using the tractable genetics of Drosophila to discover the roles of the protein in the development and cell physiology of a model insect.