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KBRIN

SGD Research/Education Network

The Kentucky Biomedical Research Infrastructure Network (KBRIN) extended it's research outreach into the undergraduate realm by implementing the Small Genome Discovery (SGD) program. The SGD program is an inclusive research-education community (iREC)1 that provides a centralized support infrastructure to enable undergraduate students from different types of institutions to engage in meaningful research. This research experience leads to publication of annotated genomes in GenBank with the students as authors. The SGD initiative fulfills KBRIN's goal, to extend the research infrastructure network within Kentucky, by supporting a variety of universities, colleges and community colleges in the mission to build a research experienced workforce. The SGD program promotes a collaborative community across Kentucky that fosters an intellectual inquiry based environment for faculty, students and their broader communities. This initiative is supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health, grant# P20GM103436. 

SGD Program Overview

The Small Genome Discovery program is a two semester set of courses. In the first course, called in situ, students isolate and purify bacteriophage from soil samples that they collect. They amplify the purified bacteriophage and isolate DNA from the phage particles. They characterize the DNA by restriction enzyme digestion and gel electrophoresis. They also visualize the morphology of their phage by electron microscopy. DNA, from at least two phages per affiliate institution, is sequenced between the first and second courses. Samples for each isolated phage is submitted to the Small Genome Discovery Support Center for archiving. During the second course, called in silico, students use our PECAAN software to predict the location of genes and tRNAs within the sequenced bacteriophage genomes. Bacteriophage genomes range between 50 and 250 genes, but most genomes average about 100 genes. Students collect evidence to support the location and function of each gene. They record their findings as annotations, which are reviewed and then published in GenBank with each student’s name as authors.

Most SGD affiliates implement both the in situ and in silico portions of this program, however, some institutions implement only the in silico portion. We have seen these program portions implemented as substitutions for labs that are currently being taught, as special separate courses, as honors laboratory sections and as special sections to engage at-risk students or even non-science majors. Evaluations of all implementations has shown that students show significant gains and an improved attitude towards science compared to traditional laboratory courses.2  If your are interested in joining the SGD community and engaging students in genome annotation, click on our SGD Community Application Form in the left menu.

SGD Annual Symposium

Each January, SGD affilliate faculty and students meet together in a Small Genome Discovery Symposium. This gives faculty the opportunity to interact and exchange ideas and tips on how they were able to implement and transition the Small Genomes program into their school. Students share their results in poster sessions and training is done on new features and protocols of the program. Students are encourages to build on their SGD experience by applying to other research programs either at their institution or through summer research programs. The SGD Symposium also allows us to invite interested faculty and students from non-affiliated schools and from the community to attend and to see how the affiliated network schools have succeeded in this program.

References

1 Hanauer, D.I., Graham, J.M., SEA-PHAGES, Betacur,L., Bobrownicki, A., Cresawn, S.G., Garlena, R.A., Jacobs-Sera, D., Kaufmann, N., Pope, W.H., Russell, D.A., Sivanathan, V., Asai, D.J., Hatfull, G.F. (2017) "An Inclusive Research-Education Community (iREC): A model for student engagement in science", PNAS in press.

2 Jordan,T. C., Burnett, S. H., Carson, S., Caruso, S. M., Clase, K., DeJong, R. J., Dennehy, J. J., Denver, D. R., Dunbar, D., Elgin, S. C. R., Findley A. M., Gissendanner, C. R., Golebiewska, U. P., Guild, N., Hartzog, G. A., Grillo, W. H., Hollowell, G. P., Hughes, L. E., Johnson, A., King, R. A., Lewis, L. O., Li,W., Rosenzweig, F., Rubin, M. R., Saha, M. S., Sandoz, J., Shaffer, C. D., Taylor, B., Temple, L., Vazquez, E., Ware, V. C., Barker, L.P., Bradley, K. W., Jacobs-Sera, D., Pope, W. H., Russell, D. A., Cresawn, S. G., Lopatto, D., Bailey, C. P., Hatfull, G. F. (2014) A broadly implementable research course for first-year undergraduate students. mBio 5:e01051-01013.