RUI: Biology-Physics Collaboration to Investigate the Genetic and Structural Basis of Competence in Bacteria

智力价值：细菌有一层类似于人类皮肤的覆盖膜，旨在将内部成分挡在里面，把异物挡在外面。一些细菌已经发展出通过这种膜输入外来DNA并将其整合到自己的基因组中的能力。这种能力被称为自然转化或能力。因为有能力的细菌可以输入从它们自己的天然DNA到动物DNA的一切东西，它们可以迅速适应紧张的环境，比如在抗生素存在的情况下。这项研究项目是为了更好地了解细菌如何能够找到DNA并将其移动到膜上。目前已知的是，一些细菌可以形成被称为IV型菌毛的结构，这种结构由穿过细胞膜的孔组成，相关的长附属物可以通过这些孔向外伸出。IV型菌毛被细菌用来在表面上拉动自己，基本上使用附属物作为可伸缩的抓钩。据信，负责能力的机构在结构上类似于IV型桩柱。这种相似性提出了两个假设：第一，构建能力机器的基因集必须与构建IV型菌毛的基因集相似，第二，能力机器执行类似于IV型菌毛的活动，尽管目的不同。这项研究将使用IV型菌毛基因来识别潜在的能力基因，然后评估这些基因是否真的参与构建能力机器。此外，原子力显微镜将被用来拍摄非常高分辨率的胜任细菌的照片，以看到胜任的机器和附属物。看看能力机器本身，就能理解一群细胞如何变得更有能力。也许当每个细胞制造更多的机器，或者当更多的细胞制造机器，或者当每台机器制造更多的附属物时，种群变得更有能力。这些图片还将表明，有能力的细菌是否会用它们的附属物来“钓鱼”，将它们扔出去，并将它们收回，将DNA移向自己。这项研究的总体目标是对细菌能力的遗传基础和物理机制产生更深入的理解。广泛的影响：所有拟议的研究都将与本科生合作进行。PI在让本科生参与研究方面有着良好的记录，在十年的时间里，他们每人都在科罗拉多学院与108名学生一起工作。这些学生中有许多是妇女和少数民族，私营部门积极招收这类学生。PI是一名物理学家和一名生物学家正在合作，预计将在实验室进行这个项目研究的十几名学生将反映出同样的专业组合。此外，PIS基于这项研究为一年级学生开发了一门生物物理学课程，最终是一个项目，学生们准备一个细菌样本，用原子力显微镜对其成像，然后写一篇期刊式的论文来展示他们的研究，从而让他们体验科学研究。在获奖期间，这一体验将提供给48名一年级学生。

Intellectual Merit: Bacteria have a covering membrane, analogous to human skin, designed to keep their internal components in and foreign bodies out. Some bacteria have developed the ability to import foreign DNA across this membrane and incorporate it into their own genomes. This ability is called natural transformation or competence. Because competent bacteria can import everything from their own native DNA to animal DNA, they can adapt rapidly in stressful environments, such as in the presence of antibiotics. This research project is to better understand how bacteria are able to find DNA and move it across their membranes. What is currently known is that some bacteria can make structures, called Type IV Pili, which consist of pores through their membranes and through which associated long appendages can project outward. Type IV Pili are used by bacteria to pull themselves across a surface, essentially using the appendages as retractable grappling hooks. The machinery responsible for competence is believed to be similar in structure to Type IV Pili. This similarity suggests two hypotheses: first, the set of genes that build the competence machine must be similar to the set of genes that build Type IV Pili, and second, the competence machine performs similar actions to Type IV Pili, albeit for a different purpose. This research will use Type IV Pili genes to identify potential competence genes and then evaluate whether those genes really do participate in building a competence machine. In addition, Atomic Force Microscopy will be used to take very high resolution pictures of competent bacteria to see both the competence machines and appendages. Looking at the competence machines themselves yields an understanding of how a population of cells becomes more competent. Perhaps populations become more competent when each cell makes more machines or when more cells makes machines or when each machine makes more appendages. The pictures will also indicate whether competent bacteria might use their appendages to "fish" for DNA by throwing them out and retracting them to move the DNA toward themselves. The overall goal of this research is to generate a much deeper understanding of both the genetic basis and the physical mechanisms of competence in bacteria.Broader Impacts: All the proposed research will take place in collaboration with undergraduate students. The PIs have a strong track record of involving undergraduates in research, having collectively worked with 108 students in ten years each at Colorado College. Many of these students were women and minorities, and the PIs actively recruit such students. The PIs are a physicist and a biologist in collaboration, and the dozen students expected to conduct research in their labs on this project will reflect this same combination of majors. In addition, the PIs developed a biophysics course for first-year students based on the research, which culminates with a project in which the students prepare a bacterial sample, image it with atomic force microscopy, and then write a journal-style paper to present their research, thus giving them an experiential taste of scientific research. This experience will be offered to 48 first-year students during the term of the award.