Semester-long inquiry-based molecular biology laboratory: Transcriptional regulation in yeast

Long non-coding RNA and ribosomal protein genes in a yeast ageing model: an investigation for undergraduate research-based learning

The unicellular yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe are widely used eukaryotic model organisms. Research exploiting the tractability of these model systems has contributed significantly to our understanding of a wide range of fundamental processes. In this article, we outline the features of yeast that have similarly been exploited for undergraduate research training. We selected examples from published literature that demonstrate the utility of the yeast system for research-based learning embedded in the curriculum. We further describe a project which we designed for the team-based final-year dissertation projects module on our transnational joint programme, which investigates whether the expression and functions of the budding yeast RPL36 ribosomal protein paralogs are influenced by the overlapping long non-coding RNA genes. Students carry out the experimental procedures in a 2-week timetabled teaching block and exercise widely applicable biochemical techniques, including aseptic yeast cell culture and sample collection, RNA isolation, qRT-PCR quantitation, protein extraction and Western blot analysis, and cell cycle progression patterns using light microscopy and flow cytometry. It is challenging to design training programmes for undergraduates that are meaningful as well as practical and economical, but it is possible to transform active research projects into authentic research experiences. We consider yeast to be an ideal model organism for such projects. These can be adapted to the constraints of course schedules and explore fundamental biochemical topics which are evolutionarily conserved from yeast to mammals.

Laboratory Exercise to Measure Plasmid Copy Number by qPCR

Quantitative PCR (qPCR) has numerous applications in biology. In an educational setting, qPCR provides students an opportunity to better understand the PCR mechanism by providing both quantitative information about the reactions and also data to troubleshoot PCRs (e.g., melt curves). Here, we present a relatively short (2-h) laboratory activity to demonstrate qPCR to quantify plasmid copy number (CN) by measuring the cycle threshold (C_T ) values for a genomic gene and a plasmid gene using transformed cells as a template. The activity can be combined with additional laboratory exercises, including bacterial transformation, to create the template to be used in the qPCRs. This lab activity is ideal for undergraduate laboratory courses that include recombinant DNA technology. (This work was presented at the 2020 Biomedical Engineering Society annual meeting).

Using Metabolic Engineering to Connect Molecular Biology Techniques to Societal Challenges

Genetically modified organisms (GMOs) are a topic of broad interest and are discussed in classes ranging from introductory biology to bioethics to more advanced methods-focused molecular biology courses. In most cases, GMOs are discussed in the context of introducing a single protein-coding gene to produce a single desired trait in a crop. For example, a commercially available kit allows students to test whether food products contain GMOs by detecting the Bacillus thuringiensis delta-endotoxin gene, which confers resistance to European corn borers. We have developed an 8-week laboratory module for upper-division undergraduates and graduate students that builds upon students’ basic understanding of GMOs to introduce them to the techniques used to sustainably produce commercially valuable products in yeast through metabolic engineering. In this course, students use recombination-based methods to assemble genes encoding entire metabolic pathways in Saccharomyces cerevisiae, perform genetic screens to identify yeast genes that impact metabolite yield, and use error-prone PCR to optimize metabolic pathway function. In parallel to these laboratory-based activities, students engage with the societal impact of these approaches through case studies of products made via yeast metabolic engineering, such as opioids, omega-3 fatty acids, and the Impossible Burger. In this report, we focus on these case studies as well as an individual sustainability project assignment created for this course. This assignment, which spans the 8-week module, asks students to find examples of yeast metabolic engineering that could be used to address current sustainability challenges in their communities. By the end of the course, students synthesize this information to create a case study that could be used to teach concepts related to metabolic engineering and sustainability to their peers. Student approaches to this project have varied from literature reviews, to news searches, to directly contacting and interviewing researchers using novel metabolic engineering approaches. These student-produced projects are used as case studies in future semesters, amplifying student voices and contributing to student ownership. While developed in the context of this course, the sustainability project and case studies are broadly applicable and could be adapted for use in biology or bioethics courses at the undergraduate or graduate level. Through this report, we hope to gain collaborators interested in implementing a version of the course at their institutions, allowing for robust assessment of the impact of the course on a larger group of students.

A modular laboratory course using planarians to study genes involved in tissue regeneration

Undergraduate research experiences are excellent opportunities to engage students in science alongside experienced scientists, but at large institutions, it is challenging to accommodate all students. To address and engage a larger number of students, we developed a modular laboratory course based on the course-based undergraduate research experiences model. This new course was integrated with the scientific aims of a research laboratory studying the cellular and molecular mechanisms underlying tissue regeneration in planarians. In this course, students were asked to identify genes with roles in planarian biology. Students analyzed and cloned an assigned gene, determined its expression pattern in situ and examined its function in regeneration. Additionally, we developed critical thinking and scientific communication skills by incorporating activities focused on critical concepts. Students obtained high quality primary data and were successful in completing and mastering the course learning outcomes. They benefitted by developing basic research skills, learning to perform, trouble-shooting experiments, reading and critically analyzing primary literature, and using the information to defend and explain their experimental results. Through this course, students also increased their confidence and ability to perform independent scientific research. The course was designed to make it accessible to the community to implement and adapt as appropriate in diverse institutions. © 2019 International Union of Biochemistry and Molecular Biology, 47(5):547-559, 2019.