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Isolation and Genomic Characterization of Novel Mycobacteriophages
Summary: Graham Hatfull's research focus is the study of mycobacteriophages—viruses that infect mycobacteria. His HHMI project uses the process of bacteriophage discovery and characterization ("phage hunting") to introduce large numbers of undergraduates and high school students to the methods of scientific research. In addition, the project is creating a community in which students mentor other students.
HHMI PROJECT SUMMARY
Original Project (2002 grant)
The 2002 grant was initiated with the hypothesis that bacteriophages (common viruses that infect bacteria) are useful for teaching because of their enormous diversity and because relatively simple techniques are needed to determine the gene sequences of new phages. Thus, bacteriophages can be used to teach substantial numbers of undergraduate and high school students, including those who have had little technical experience in the lab and those who are not necessarily high academic achievers but who might have the potential for scientific creativity. Each student works on isolating a new bacteriophage, determining its genome sequence, and comparing it with known genomes. It is hoped that students will coauthor a peer-reviewed publication. In the process of doing their research, students learn about microbiology ecology, genetics, biochemistry, and evolution. Moreover, by taking ownership of a sequencing project and learning what scientists do, students come to understand that they, too, can become scientists. Along with performing research, students are also teaching: Graduate students and postdoctoral fellows mentor undergraduates, and undergraduates mentor high school students. During the initial grant period, more than 20 undergraduates and 85 high school students conducted in-depth bacteriophage research and identified more than 30 new phages. The program structure was modified to introduce phage hunting to entire high school classrooms, reaching more than 1,200 students.
Project Update (2006 grant)
We will continue to use the phage-hunting model to train undergraduates and high school students in my lab. HHMI investigator William R. Jacobs at the Albert Einstein College of Medicine, with whom I often collaborate on my research, will continue to work with my students on their phage-hunting projects. The program will also be extended to provide experiences in phage discovery to more high school classrooms at the local and national levels, which will also provide more undergraduates with great mentoring experiences. In addition, we will use the phage-hunting program to explore how students transition successfully from novice to expert in the research lab and determine how research experiences can be optimized to train students in a research environment. To this end, we will collaborate with applied linguist Dr. David Hanauer at the Indiana University of Pennsylvania to develop a learning model that uses coded videotapes. This program element will also offer a method for assessing the educational benefits of using the phage-hunters program in the research laboratory.
RESEARCH SUMMARY
My research focus has been the study of mycobacteriophages. Studying mycobacteriophages promises not only to enhance the understanding of mycobacterial diseases but to reveal novel biological processes hidden in the enormous diversity of the microbial world. My lab's initial studies focused on a single mycobacteriophage, L5. Determination of its genome sequence revealed its overall genomic architecture and offered hints about its biological properties. We investigated in further detail the mechanism of integration and excision as well as the regulation of gene expression. These detailed investigations yield two outcomes: One is the discovery of novel biological mechanisms and the other is the development of genetic tools for mycobacterial genetic manipulation. For example, dissection of the integration apparatus has offered new insights into the control of directionality of site-specific recombination events, and it has enabled researchers in my lab to develop integration-proficient vectors in which any gene can be stably integrated—in single copy—into mycobacterial chromosomes with high efficiency. Likewise, our study of immunity regulation in L5 has revealed a new mechanism for genomic transcriptional silencing and also generated nonantibiotic selectable markers for use in vaccine development.
My lab has also exploited two key features of bacteriophages: their abilities to infect their hosts specifically and efficiently. As such, they make superb delivery systems, and they have been used as transposon delivery vehicles and also as the basis for novel diagnostic systems. For example, we have constructed luciferase reporter mycobacteriophages that carry the firefly luciferase gene and used them for rapid drug susceptibility testing of clinical isolates of M. tuberculosis. About five years ago, we began to analyze additional mycobacteriophages. This was motivated by two main concerns. First, although L5 was a good model system, it offered a limited view of mycobacteriophage biology. Second, although L5 offered some interesting insights into the processes of phage evolution, it was clear that, to address these questions, additional phage genomes needed to be analyzed. We have characterized mycobacteriophages D29, TM4, Bxb1, and Bxz1.
To further explore bacteriophage diversity and evolution, we have begun to isolate a new collection of mycobacteriophages and to characterize them at the genomic level. Using a medium throughput sequencing approach, it is possible to determine many phage genomes in an expeditious manner and analyze them by bioinformatic methods. Moreover, we are finding mycobacteriophage-encoded genes that are predicted to play key roles in the biology of their mycobacterial hosts, providing new insights into the genetics of tuberculosis.
Last updated March 2007
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