Functional Genomics and Proteomics: Applications to Immunobiology
The interdisciplinary course “Functional Genomics and Proteomics: Applications to Immunobiology” a core component of IBVS training grant was taught in the Spring of 2016. The IBVS flagship course is required for all graduate and postdoctoral trainees supported by the training grant as we consider it an essential component of their training. The course is also open to all graduate and postdoctoral trainees at Vanderbilt University School of Medicine
This year’s course had 14 trainees; 9 graduate students and 5 postdoctoral fellows. The first three weeks of the course focused on the interpretation and application of “big data” in Immunobiology (Schultze, 2015). Dr. Link employed a hands-on approach using open-source software applications to process, analyze, and interpret next-generations RNA-Seq and proteomics data. During the 3 weeks, the class used the online analysis programs Galaxy and the Global Proteome Machine to process and analyze RNA-Seq and mass spectrometry-based proteomics data acquired from primary immune cells after vaccination with an influenza vaccine (Hoek et al., 2015). The goal was to identify and functionally analyze RNA transcripts and proteins that significantly change in primary human immune cells after vaccination.
The second part of the 2016 course was taught by the IBVS faculty members: Jack Hawiger, Luc van Kaer, Meena Madhur, James Crowe, James (“Tom”) Thomas, Mark Boothby and Peggy Kendall. Each faculty members selected a publication in immunobiology that applies functional genomics or proteomics approaches to an immunological question (Becattini et al., 2015; DiGiandomenico et al., 2014; Huan et al., 2015; Human Microbiome Project, 2012; Li et al., 2014; Vahedi et al., 2015; van Haren et al., 2011). The IBVS faculty preceptor presented a lecture to the class on the publication’s immunobiology, background, and functional genomics approach. Later in the week, the preceptor and students met to critically discuss the strengths and weaknesses in the publication. The discussion was driven primarily by the students. The faculty mentor served to facilitate the discussion, answer questions, provide broader insights, and evaluate the students. Below is the list of faculty-selected publications used for the 2016 IBVS course.
For a final exam, each student selected a publication from the literature that used either a functional genomics or proteomics approach to address an important problem in immunobiology. A grade was given each week based on active participation presenting figures and the general discussion (70% of final grade). The student’s presentation represented 30% of their final grade.