How golden is silence? Teaching undergraduates the power and limits of RNA interference

Investigating Student Engagement and Making Science Real during a Pandemic: Bioskills at Home, a Case Study

Development of key practical skills is fundamental to bioscience courses in higher education. With limitations on access to laboratory time due to the COVID-19 pandemic, a “Bioskills at home” kit was developed to create opportunities for first year undergraduate students to develop these skills using online support resources to guide their activities and build communities of learning. Equipment and activities in this kit enabled students to practice key skills such as pipetting, data handling, experimental design and microscopy, as well as build an online peer learning community through the use of discussion boards and microscopy competitions that encouraged students to explore their local environment. Students who engaged with these activities reported increased confidence in key practical skills. Practical assessment of skills showed that that there was no reduction in the proportion of students who succeeded in achieving the pipetting learning objective compared to previous years, despite a significantly reduced on-campus provision. Although the celebration event to choose the microscopy competition winners was well attended, there was limited use of the discussion boards by students to build a community of learning during the term. Refinement of this initiative will focus on providing greater scaffolding to encourage greater engagement with activities and enhance community building.

siRNA Immunological Fishing Training (SIFT) Experience as a Novel Research Education Tool for Students Studying Immunology

This report describes an innovative research education tool for student exposure and training in immunology. Utilizing the wealth of transcriptomics data provided through the immunological genome project, graduate and undergraduate students can engage in hands-on experimental studies to identify and rigorously characterize novel genes in immune cells using RNA interference-mediated approaches. The SIFT activities are directly aligned with cell biology and immunology courses and serve to reinforce and expand on the foundations learned. Furthermore, the student-driven studies provide a sense of ownership and largely expose students to the breadth of experimental research approaches in the biological sciences. Finally, generation of original datasets supports the greater scientific community by contributing in assembly and delineation of the regulatory networks that govern immunity.

Killing two birds with one stone: Model plant systems as a tool to teach the fundamental concepts of gene expression while analyzing biological data

Plants are ideal systems to teach core biology concepts due to their unique physiological and developmental features. Advances in DNA sequencing technology and genomics have allowed scientists to generate genome sequences and transcriptomics data for numerous model plant species. This information is publicly available and presents a valuable tool to introduce undergraduate students to the fundamental concepts of gene expression in the context of modern quantitative biology and bioinformatics. Modern biology classrooms must provide authentic research experiences to allow developing core competencies such as scientific inquiry, critical interpretation of experimental results, and quantitative analyses of large dataset using computational approaches. Recent educational research has shown that undergraduate students struggle when connecting gene expression concepts to classic genetics, phenotypic analyses, and overall flow of biological information in living organisms, suggesting that novel approaches are necessary to enhance learning of gene expression and regulation. This review describes different strategies and resources available to instructors willing to incorporate authentic research experiences, genomic tools, and bioinformatics analyses when teaching transcriptional regulation and gene expression in undergraduate courses. A variety of laboratory exercises and pedagogy materials developed to teach gene expression using plants are discussed. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

A critical analysis of assessment quality in genomics and bioinformatics education research

The growing importance of genomics and bioinformatics methods and paradigms in biology has been accompanied by an explosion of new curricula and pedagogies. An important question to ask about these educational innovations is whether they are having a meaningful impact on students' knowledge, attitudes, or skills. Although assessments are necessary tools for answering this question, their outputs are dependent on their quality. Our study 1) reviews the central importance of reliability and construct validity evidence in the development and evaluation of science assessments and 2) examines the extent to which published assessments in genomics and bioinformatics education (GBE) have been developed using such evidence. We identified 95 GBE articles (out of 226) that contained claims of knowledge increases, affective changes, or skill acquisition. We found that 1) the purpose of most of these studies was to assess summative learning gains associated with curricular change at the undergraduate level, and 2) a minority (<10%) of studies provided any reliability or validity evidence, and only one study out of the 95 sampled mentioned both validity and reliability. Our findings raise concerns about the quality of evidence derived from these instruments. We end with recommendations for improving assessment quality in GBE.

A laboratory-intensive course on RNA interference and model organisms

RNA interference (RNAi) is a powerful method to silence gene expression in a variety of organisms and is generating interest not only as a useful tool for research scientists but also as a novel class of therapeutics in clinical trials. Here, we report that undergraduate and graduate students with a basic molecular biology background were able to demonstrate conceptual knowledge and technical skills for using RNAi as a research tool upon completion of an intensive 8-wk RNAi course with a 2-h lecture and 5-h laboratory per week. Students were instructed on design of RNAi experiments in model organisms and perform multiweek laboratory sessions based on journal articles read and discussed in class. Using Nicotiana benthamiana, Caenorhabditis elegans, and mammalian cell culture, students analyzed the extent of silencing using both qualitative assessment of phenotypic variations and quantitative measurements of RNA levels or protein levels. We evaluated the course over two semesters, each with a separate instructor. In both semesters, we show students met expected learning outcomes as demonstrated by successful laboratory experiment results, as well as positive instructor assessments of exams and lab reports. Student self-assessments revealed increased confidence in conceptual knowledge and practical skills. Our data also suggest that the course is adaptable to different instructors with varying expertise.

Genome Consortium for Active Teaching: meeting the goals of BIO2010

The Genome Consortium for Active Teaching (GCAT) facilitates the use of modern genomics methods in undergraduate education. Initially focused on microarray technology, but with an eye toward diversification, GCAT is a community working to improve the education of tomorrow's life science professionals. GCAT participants have access to affordable microarrays, microarray scanners, free software for data analysis, and faculty workshops. Microarrays provided by GCAT have been used by 141 faculty on 134 campuses, including 21 faculty that serve large numbers of underrepresented minority students. An estimated 9480 undergraduates a year will have access to microarrays by 2009 as a direct result of GCAT faculty workshops. Gains for students include significantly improved comprehension of topics in functional genomics and increased interest in research. Faculty reported improved access to new technology and gains in understanding thanks to their involvement with GCAT. GCAT's network of supportive colleagues encourages faculty to explore genomics through student research and to learn a new and complex method with their undergraduates. GCAT is meeting important goals of BIO2010 by making research methods accessible to undergraduates, training faculty in genomics and bioinformatics, integrating mathematics into the biology curriculum, and increasing participation by underrepresented minority students.