CURE on yeast genes of unknown function increases students' bioinformatics proficiency and research confidence

• Published in: Journal of microbiology & biology education 2024-04, Vol.25 (1), p.e0016523-e0016523
• Main Authors: Miller, Mary, Tobin, Tammy, Aiello, David P, Hanson, Pamela, Strome, Erin, Johnston, Stephen D, Issel-Tarver, Laurie, Kushner, David B, Keeney, Jill B
• Format: Article
• Language: English
• Subjects: CURE; Curriculum; gene deletion; gene exploration; hypothesis formation; Saccharomyces cerevisiae; yeast
• ISSN: 1935-7877; 1935-7885
• DOI: 10.1128/jmbe.00165-23

Course-based undergraduate research experiences (CUREs) can reduce barriers to research opportunities while increasing student knowledge and confidence. However, the number of widely adopted, easily transferable CUREs is relatively small. Here, we describe a CURE aimed at determining the function of poorly characterized genes. More than 20 years after sequencing of the yeast genome, nearly 10% of open reading frames (ORFs) still have at least one uncharacterized Gene Ontology (GO) term. We refer to these genes as "ORFans" and formed a consortium aimed at assigning functions to them. Specifically, over 70 faculty members attended summer workshops to learn the bioinformatics workflow and basic laboratory techniques described herein. Ultimately, this CURE was adapted for implementation at 34 institutions, resulting in over 1,300 students conducting course-based research on ORFans. Pre-/post-tests confirmed that students gained both (i) an understanding of gene ontology and (ii) knowledge regarding the use of bioinformatics to assign gene function. After using these data to craft their own hypotheses, then testing their predictions by constructing and phenotyping deletion strains, students self-reported significant gains in several areas, including computer modeling and exposure to a project where no one knows the outcome. Interestingly, most net gains self-reported by ORFan Gene Project participants were greater than published findings for CUREs assessed with the same survey instrument. The surprisingly strong impact of this CURE may be due to the incoming lack of experience of ORFan Project participants and/or the independent thought required to develop testable hypotheses from complex data sets.