PgmNr E8016: Yeast orphan gene project: Finding a place for ORFans to GO.

Authors:
J. B. Keeney 1 ; E. Strome 2


Institutes
1) Juniata College, Huntingdon, PA; 2) Northern Kentucky University, Highland Heights, KY.


Abstract:

When the genomic sequence of the model eukaryote Saccharomyces cerevisiae was completed in 1996, the expectation was that an understanding of the integrated functioning of the collection of genes in this single-celled eukaryote would shortly follow.  Despite almost 20 years of intense collaborative effort among yeast researchers, nearly 10% of open reading frames (ORFs) are considered uncharacterized.  Determining the function of these orphan genes (ORFans) will require mining the current yeast genomic data, compiled in the Saccharomyces genome database (SGD), to most effectively design ORF-specific experiments in cell and molecular biology, and comparative genomics. A network of yeast researchers/educators with a focus on teaching experimental design could help overcome the challenges and absorb the risks of researching individual ORFans. The goal of the proposed Yeast Orphan Gene Project is to organize a consortium of undergraduate researchers and faculty at primarily undergraduate institutions (PUIs) to coordinate resources and design strategies to assign molecular functions to S. cerevisiae ORFans. Ultimately, the yeast orphan gene project aims to use the process of determining orphan gene function as a tool to teach undergraduate students key concepts in bioinformatics, genomics, molecular biology, and genetics and impart valuable experience in scientific collaboration and leadership. Based on analysis of SGD information, students will design and execute ORF specific experiments for defining gene function. The network will facilitate collaboration between students at different institutions so that students can share strategies and technique solutions while developing experience in on-line collaborations. These skills, including the ability to (1) apply the process of science, (2) use modeling and simulation, and (3) communicate and collaborate, are core competencies in “Vision and Change”. The proposed network will prepare undergraduates for careers in STEM, provide tools for faculty at PUIs to expand research experience for undergraduates, and incorporate research experiences into undergraduate courses. It will also be a mechanism to distribute a tested model of an authentic course-based research experience to a diverse set of institutions by providing workshop and assessment support. The networking activities will expand the expertise of faculty, as well as provide undergraduates tools and resources for collaboration. Defining the function of yeast ORFans will advance the goal of the yeast community to determine the function of the entire set of annotated yeast ORFs.