Introduction of Bioinformatics in an Undergraduate Molecular Techniques Laboratory using Extreme Halophiles as Models

生物科学（61）本项目将生物信息学和微阵列分析的研究工具作为教学方法。这一建议的智力价值解决了生物信息学所需的技术基础设施问题，在现有的大学生分子技术实验室中引入了两项基于调查的实验：从环境中分离的新型极端嗜盐菌中回收的16 S rRNA基因的DNA测序和伴随的系统发育分析;利用基因芯片技术研究极端嗜盐古菌Halobacterium sp. NRC-1的基因表达差异。DNA测序/系统发育研究的目标是：（i）PCR扩增来自极端嗜盐生物的16 S rRNA基因，这些生物是学生从附近的盐矿中分离出来的，（ii）对这些基因进行测序并将序列提交给GenBank，以及（iii）根据这些序列将生物体进行系统发育。微阵列分析的目的是：（i）设计和实施差异基因调控实验，（ii）提取和标记RNA，（iii）探测，扫描和分析来自盐杆菌NRC-1的DNA微阵列，以及（iv）确定哪些基因在实验条件下差异表达。这一提议的更广泛影响包括：（i）使用基于探究的教学和学习来推进发现和理解，（ii）通过将当前关于极端嗜盐生物的研究调整到本科教学实验室来整合研究和教育，（iii）通过购买仪器来加强技术教育基础设施，以及（iv）通过万维网、基因库、在同行评审的科学教育期刊上发表文章，并在专业协会的教育部门发表演讲。

Biological Sciences (61) This project is adapting research tools in bioinformatics and microarray analysis as a teaching method. The intellectual merit of this proposal addresses the problem of the technical infrastructure required for bioinformatics by introducing into an existing undergraduate molecular techniques laboratory two inquiry-based experiments: DNA sequencing and concomitant phylogenetic analysis of 16S rRNA genes recovered from novel extreme halophiles isolated from the environment; and global differential gene expression in the extremely halophilic archaeon Halobacterium sp. NRC-1 by DNA microarray analysis. The objectives for the DNA sequencing/phylogenetic study are: (i) PCR amplification of 16S rRNA genes from extremely halophilic organisms the students isolate from a nearby salt mine, (ii) sequencing these genes and submitting the sequences to GenBank, and (iii) placing the organisms phylogenetically based upon these sequences. The objectives for the microarray analysis are: (i) designing and implementing differential gene regulation experiments, (ii) extracting and labeling RNA, (iii) probing, scanning and analyzing DNA microarrays from Halobacterium NRC-1, and (iv) determining which genes are differentially expressed under the experimental conditions. The broader impacts of this proposal include: (i) advancing discovery and understanding using inquiry-based teaching and learning, (ii) integrating research and education by adapting current research on extreme halophiles into an undergraduate teaching laboratory, (iii) enhancing the technical educational infrastructure with the acquisition of instrumentation, and (iv) disseminating the results through the world wide web, GenBank, articles in peer-reviewed journals of science education, and presentations at the education divisions of professional societies.