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KBRIN SGD Program

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

We encourage affiliates to implement both the in situ and in silico portions of this program at your institution, however, if your institution does not have the equipment to support the in situ portion of the program (see equipment survey on the application form), please consider at least implementing the in silico portion of the Small Genome Discovery program. We have seen this program 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 non-science majors. You will need to decide how this program can best be implemented for the benefit of your students.

Each January, following the two courses, two faculty and two students will be invited to present their results in a Small Genome Discovery Symposium. This will give 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. This will also allow us to invite non-affiliated schools to attend and to see how the affiliated network schools have succeeded in this program.

SGD Workflow

SGD Program Funding

A week-long workshop for two faculty members will be provided to new affiliate institutions implementing this program. Housing, travel, and meals will be covered up to the budgeted limits. This workshop will give faculty hands-on in situ and in silico course experience.

Each institution will be provided with classroom supplies for the course for the first two years. Following the first two years of support, you are expected to transition the supply cost either to student lab fees or find other avenues of support within your institution. 
The electron microscopy and DNA sequencing will be funded each year by the SGD program grant for the entire length of the granting period (through 2019). Electron microscopy (20 phage samples/year/institution) and phage genome DNA sequencing (2 genomes/year/ institution) will be covered by the SGD program grant.

Travel and housing costs for the annual Small Genome Discovery Symposium will be covered up to the budgeted limit set by the SGD program.

SGD Program Expectations

Each institutional affiliate will be expected to implement the SGD course material in one or more classes and recruit students into the program. Each institution will

If you are interested in joining the KBRIN Small Genome Discovery program, please fill out an application form.