This RCN-UBE project aims to greatly expand the incorporation of authentic genomics, bioinformatics, and functional genomics research into the undergraduate curriculum by providing training workshops, an updated Web-based genome re-annotation platform and a collaborative support network to faculty members at 2- and 4-year colleges and universities across the U.S. Biology has been transformed by the exponential increase in genomic information, but the value of that information hinges upon accurate predictions of gene function (annotation) and experimental evaluation that tests those predictions. The network will empower faculty to engage students in the concepts, skills, and experimental thinking that not only increases student scientific literacy and problem-solving abilities but also allows them to contribute to science and society right now through the deeper second-pass annotation of large numbers of genes in microbial genomes and experimental testing of predicted gene function.
Network training workshops will be based on a geographic node model wherein groups of nearby participants agree on a common meeting site and time, and then one or more trainers travel to that site to run a weekend workshop. Each workshop will focus on either (a) gene annotation (genomics and bioinformatics) and functional prediction or (b) experimental testing of gene function (functional genomics). Training in gene annotation will be broken down into several modules such as sequence similarity searches and prediction of protein localization, and will involve appropriate freely available bioinformatics tools. The use of a freely available Web platform for re-annotation of genomes from Bacteria and Archaea (GENI-ACT) allows for users to easily construct, assign, and manage gene annotations across a large number of students in multiple courses. Virtual lab notebooks for each gene annotation allow individual or collaborative work in collecting and analyzing data. The platform capability includes students combining their own bioinformatics analyses with data from the research literature and their own functional genomics efforts to reach conclusions and make the data available for the larger research community and public. Workshops on functional genomics will focus on how to bring together well-known (e.g., transposon mutagenesis, PCR) and more specialized lab strategies (e.g., site-directed mutagenesis, protein overexpression) within the context of laboratory courses to test the predicted function of genes. Participants will be encouraged to brainstorm with trainers and other participants on appropriate strategies for non-model bacterial strains and genes of interest to them. Participants will be encouraged to form collaborations within and between nearby institutions using a freely available Web teaching/research support structure (GENI-SCIENCE). Further cross-fertilization of ideas and support are provided by the network using social media tools.
This project is being jointly funded by the Directorate for Biological Sciences (BIO), Division of Biological Infrastructure, and the Directorate for Education and Human Resources (EHR), Division of Undergraduate Education as part of their efforts to address the challenges posed in Vision and Change in Undergraduate Biology Education: A Call to Action (http://visionandchange.org/finalreport/). This project is also co-funded by the Division Molecular and Cellular Biosciences (MCB) in the BIO directorate.
