A Caenorhabditis elegans lab module provides experiential learning for molecular genetics students

ABSTRACT

Caenorhabditis elegans is an established biological model that is used as a genetic tool due to its many advantages, such as short life cycle, small size, and availability of mutant strains. I describe here a 7-week C. elegans lab module that was designed for an upper-level molecular genetics course. Students measured gene expression by using fluorescence microscopy and RT-qPCR assays, and they evaluated how genes influence animal behavior and aging by using chemotaxis and survival assays. To observe how genotypes influence phenotypes, wild-type and mutant worms, including mutants expressing green fluorescent protein, were used. Most of the students reported that they “liked/loved” all lab activities on microscopy, behavioral assay, survival analysis, RNA extraction, cDNA synthesis, qPCR, and data analysis in a post-survey using a 5-point Likert scale. Students also “agreed/strongly agreed” that they understood several genetic concepts, including “genotype vs. phenotype,” “mutation,” and “model organisms,” and how these concepts apply to these lab activities. Although students expressed that they faced some challenges in counting worms in a stereomicroscope and in interpretation of variable data, they valued the variety of techniques, as well as the consistency and sequencing of this lab module. Overall, students appreciated the hands-on skills acquired by using C. elegans to explore concepts of genetics and molecular biology.

INTRODUCTION

Caenorhabditis elegans is an established invertebrate model that has been used as a genetic tool to understand the function of genes in basic and applied sciences. This animal model has also been used in several diverse undergraduate lab courses that range from molecular genetics to cell biology and neuroscience (1–5). The ease of culturing C. elegans with open-source protocols (6), their low-handling risk, and minimal equipment requirements make this model ideal for teaching undergraduates. Here, I describe a 7-week C. elegans-based laboratory module that aims to introduce students to C. elegans as a genetic model organism by applying molecular genetics techniques to link genotypes with phenotypes.

One of the advantages of this lab module is that it enables students to observe phenotypic changes at different levels, as visual representations of genetics concepts are critically important for students' learning processes (7, 8). This lab module starts with microscopy-based activities and builds upon this foundation to include the observation of animal behavior and survival. Once C. elegans as an in vivo model has been experienced by the students, it becomes easier to interpret and discuss abstract concepts like gene expression, which can be changed due to genetic and environmental factors. Thus, this lab module provides direct visualization of the subjects under study to enhance student engagement and establish a stronger conceptual foundation for subsequent molecular biology assays involving RNA and DNA molecules, rather than using mock samples that mimic scientific scenarios. Moreover, this lab module facilitates the connection between organisms and molecular processes, highlighting the importance of genes for human health in addition to the practice of traditional molecular biology techniques.

This lab module has its learning goals and outcomes based on the CourseSource Genetics Learning Framework (https://qubeshub.org/community/groups/coursesource/courses/genetics) developed by the Genetics Society of America’s Education Committee. The learning objectives, student outcomes, and timeline for each lab activity are stated in Table 1. By the end of the module, students will:

TABLE 1.

Learning objectives, student outcomes, and timeline for each lab activity

Lab activity	Timeline (duration)	Associated learning objectives	Student outcomes
Microscopy	Week 1 (2–3 h)	1, 2, 3	Practice wet lab skills by pipetting and making solutions. Use stereomicroscope and fluorescence microscope to observe morphology, life stage, and gene expression. Use NCBI and Wormbase databases to search for gene functions.
Behavioral assays	Week 2 (2–3 h)	1, 2, 3	Practice microscope and wet lab skills. Explain the use of behavioral (chemotaxis) assays to investigate gene function relating to human genes.
Survival analysis	Week 3 (2–3 h)	1, 2, 3	Practice microscope and wet lab skills. Explain the relevance of genes to survival of worms under stress (heat or oxidative stress). Identify interventions that change the survival-related gene expression by searching on PubMed database.
RNA extraction	Week 4 (2–3 h)	3	Practice wet lab skills and chemical safety. Use NanoDrop spectrophotometer to measure RNA concentration and purity. Perform RNA extraction protocol by using organic solvents.
cDNA synthesis	Week 5 (2–3 h)	3	Practice wet lab skills. Calculate volumes of RNA needed for a cDNA synthesis based on NanoDrop measurements. Explain the role of reverse transcriptase in cDNA synthesis for further qPCR assay.
qPCR	Week 6 (2–3 h)	3	Practice wet lab skills. Calculate volumes of cDNA and other qPCR components needed for qPCR reaction. Explain the main principles and steps of qPCR.
Data analysis	Week 7 (2–3 h)	1, 2, 3	Analyze gene expression of fluorescence microscopy data using ImageJ. Analyze and summarize data in graphs by using Excel. Calculate mean, standard deviation, and standard errors. Explain the sources of variation, and discuss the credibility of data.

1. Evaluate how genes and the environment influence phenotypes;

2. Justify how studies with C. elegans are relevant to studying human genes and genetic diseases;

3. Apply experimental methods to collect, analyze, and interpret biological data by using microscopy, behavioral, survivability, and qPCR assays.

PROCEDURE

Course context

This lab module was created for undergraduate students who have a fundamental knowledge of genetics and basic wet-lab techniques (e.g., pipetting and preparing solutions). These wet-lab techniques assist with the execution of this lab module, even though they are not directly taught in this lab module. This lab module stands on its own without accompanying lectures, as each lab class starts with an overview of the activity to be performed by the students. The students’ outcomes are assessed by their performance, answers to the worksheets’ study questions (Appendix 1, Supplemental Material), and lab notebook with purposes, protocols, results, and conclusions.

Safety issues

It is important to note that standard BSL-1 laboratory practices should be followed, and fume hoods should be used when handling organic solvents. Students should be trained in the best practices on biosafety and aseptic techniques since they handle microbial organisms (Appendix 2, Supplemental Material).

Overview

The 7-week labs (2–3 h each) are divided into the following: microscopy, behavioral assays, survival analysis, RNA extraction, cDNA synthesis, qPCR, and data analysis. The microscopy lab introduces C. elegans as a model organism, where at first, students observe their morphology, life stages, and locomotion. By using stereomicroscope and fluorescence microscope, students not only start to practice these techniques but also they are able to connect fluorescent gene expression in C. elegans with human gene homologs. Those skills are reinforced in the next two labs, when students continue to practice microscopy. Students relate their observations to physiological processes, such as the worm's ability to move toward or against volatile chemicals (behavioral assay: chemotaxis) and ability to survive against stress (survival analysis). Since C. elegans have all its neurons already elucidated, and certain stress-related genes have human homologs, students use genetic knockout mutants to predict a gene’s biological relevance to stress resistance, developmental, and/or neurobiological defects. In the following three sequential lab classes, students focus on the chemistry of traditional molecular biology assays and nucleic acids using C. elegans samples. The guanidinium chloride method to extract RNA gives the students a valued visual aid that enables them to enhance their pipetting skills and chemical safety. The cDNA synthesis and qPCR assays also reinforce the best practices for working in a wet lab while learning the principles of those methods. Lastly, students learn how to build graphs (Appendix 3, Supplemental Material) for each of the previous labs by using their own data in Excel, followed by a discussion of their variation, limitations, and interpretations.

Modifications

Instructors who adopt this lab module may want to include different techniques within the C. elegans lab module, such as, for example, using transformed bacteria to feed C. elegans with RNAi, described by others (2). Also, they may involve students in the decision of which mutants to be used in the execution of this lab module by adding experimental design and literature review before this lab module. The RNA extraction method can be replaced with a filter-based spin columns method in case fume hoods are not available.

CONCLUSION

This preliminary evaluation using a post-survey (Appendix 4, Supplemental Material) suggests that students value the use of C. elegans as an educational tool to learn molecular genetics. Most of the students (53–86%) reported that they liked/loved all lab activities, with a little more negative feelings on data analysis, behavioral assay, and survival analysis (Fig. 1A). Moreover, students perceived an enhancement of their hands-on, problem-solving, and critical thinking skills (Fig. 1B) and in their understanding of certain genetic topics/concepts (Fig. 1C). Further formal assessments of the understanding of these concepts are needed to evaluate the effectiveness of this lab module. In the open-ended feedback questions (Appendix 5, Supplemental Material), students mentioned the hands-on experience, the use of the model or techniques as the most valuable aspect of these lab classes. For example, a student mentioned that “being able to see the direct effects of genetic mutations in a model organism made concepts much clearer.” Although this is not a direct assessment of the success of learning outcomes, and a pre- and post-survey would be more informative than the post-survey alone, these results corroborate with the fact that visual representations of genetics concepts are important for student learning processes (7, 8).

Fig 1.

Respondent rating on preference/interest of each lab class (A), development of skills (B), and understanding of a topic/concept (C). Each lab section had an enrollment of 7–16 students who had taken a genetics course as a prerequisite (n = 41–44). The post-survey (Appendix 4, Supplemental Material) had the following questions: rate the following C. elegans lab units based on your level of preference or interest (A); rate the extent to which the C. elegans laboratory activities helped you develop the following skills (B); how well do you agree with this statement “I understand this ‘topic/concept,’ how it applies to the C. elegans lab units, and I can apply the knowledge of this topic to other contexts.” (C).

One of the challenges of this lab module is the data analysis and interpretation, especially when an experiment fails. For the behavioral and survival assays, the handling of the worms, environmental factors, and sensitivity of assay are factors that contribute to the variability. However, that is a valuable opportunity to discuss the biological variations and limitations of organism models. The “failure” increases the ability of students to critically think about scientific inquiry, even if they are not part of the experimental design. Therefore, this lab module enables the evaluation of studies using model organisms in genetics while fostering the development of critical problem-solving skills. In summary, students who participated in these C. elegans-based laboratory activities enhanced their understanding of genetics and acquired hands-on and wet-lab skills that can be applied in different fields in biology.

ETHICS APPROVAL

The survey data were approved by the Kean University Institutional Review Board (IRB-FY2025-51).

SUPPLEMENTAL MATERIAL

The following material is available online at https://doi.org/10.1128/jmbe.00108-26.

Supplemental material. jmbe.00108-26-s0001.pdf.

Appendix 1, worksheets; Appendix 2, materials; Appendix 3, representative graphs; Appendix 4, post-survey; and Appendix 5, responses to post-survey open-ended questions.

ASM does not own the copyrights to Supplemental Material that may be linked to, or accessed through, an article. The authors have granted ASM a non-exclusive, world-wide license to publish the Supplemental Material files. Please contact the corresponding author directly for reuse.