Engaging students in a genetics course-based undergraduate research experience utilizing Caenorhabditis elegans in hybrid learning to explore human disease gene variants

Students in the Undergraduate Biology Program at Jacksonville State University (Jax State) complete a diverse biological sciences training plan. This plan is guided by a concentration that students self-select based on their training and career interests. Biology majors and minors are required to complete a basic core curriculum, including ecology, genetics, cell biology, and senior seminar. The GENE-CURE is offered as a 300-level genetics course taken after a year of introductory biology courses and labs, typically during the second or third year of undergraduate study.

The GENE-CURE was designed and offered to students to introduce them to authentic research practices and genetic techniques. We suggest that it can be offered in any year during undergraduate or graduate training with necessary modifications. This workflow can also be utilized to train technical skills in bioinformatics and genetics.

The course was 4 credit hours and met three times a week, including two class sessions (1.5 hours each) and one lab session (2 hours). Due to the COVID-19 pandemic and transitions in learning modalities, the course was taught in different formats over four semesters (Table 1).

During Fall 2020, the course was offered hybrid synchronous. Students met virtually through Microsoft Teams. Time was split between large group discussions and break-out sessions for small group collaborative time. In-person “wet lab” sessions were offered to students inside and outside of normal class and lab time. For Spring 2021, the course was offered hybrid synchronous utilizing the same organization with a rotation schedule for in-person and virtual participation for all research sessions. During Fall 2021 and Spring 2022, the course was offered in person and consisted of the same organization.

The time spent by students and instructors on research tasks is summarized in Table 2. There are tasks specific for the instructors to ensure the progression of experiments across research sessions. Students and instructors also spent time outside of the scheduled research sessions to troubleshoot and repeat experiments to achieve specific research goals. This outside time was coordinated through reserved sessions and varied between individual students. At the start, students complete a set of online training modules focused on responsible conduct of research (RCR), basic lab safety, and other related areas (Table 2; Appendix 1).

The GENE-CURE has been primarily led by an instructor and supported by graduate and undergraduate students. Due to the COVID-19 pandemic and transitions in learning modalities, the instruction team varied across the semesters depending on the type of support available (Table 1). The instructional team ranged from the instructor to a graduate teaching assistant (GTA) to a graduate online learning assistant (GOLA) to undergraduate peer instructors. The GTAs were assigned and fulfilled their teaching assistance for their assistantship. The GOLA enrolled in a 2-hour graduate biology elective and assisted in the hybrid learning environment. The peer instructors are undergraduates who have successfully completed the GENE-CURE and want to serve as mentors. The instructor has genetics and molecular biology expertise along with experience with C. elegans husbandry and the CRISPR-Cas9 technology. GTAs were trained by the instructor on molecular genetic techniques and nematode manipulation. Undergraduate peer instructors were trained initially in the GEE-CURE.

Students were required to have at least 1 year of introductory biology knowledge and experience. This includes two introductory biology courses and subsequent labs. The first course is an introduction to the concepts of biology, including cellular structure and function, bioenergetics, patterns and mechanisms of inheritance, the processes of evolution, and ecology. The second course is an introduction to the concepts of biodiversity, from bacteria to plants and animals, with an emphasis on their structure, function, and ecological interactions. Students also enroll in two introductory labs that engage in basic biology topics.

The GENE-CURE was designed to engage students in authentic research for the development of basic research skills and to address a scientific question of interest to the students, instructor, and the scientific community. For numerous students, this was their first exposure to scientific research. Student learning objectives (SLOs) focused on three major scientific practices, including experimentation, writing, and presentation (Table 3). SLOs were evaluated with formative and/or summative assessments.

Students work and collaborate in research groups (two to six members per group) in a series of workshop-style research sessions, modules, and “wet lab” sessions. Students have ample time to conduct background literature research, construct scientific hypotheses, and design and execute experiments. An array of formative and/or summative assignments are assessed for mastery of learning objectives and research progress (Fig. 1; Appendix 4). Brainstorming and peer and instructor feedback are incorporated across all assessments.

Students are required to complete a set of online training modules, including basic lab safety. Students are required to read, acknowledge, and accept the Jax State Student Laboratory Safety Manual. Both requirements align with the American Society for Microbiology Guidelines for Biosafety in Teaching Laboratories, specifically for working with BSL-1 microorganisms (27). Students used OP50-1 Escherichia coli to feed and propagate C. elegans that need to be handled using safe practices and do not pose a biohazard risk. The appropriate personal protective equipment was worn by students while performing their experiments, including lab coats, gloves, closed-toed shoes, and protective eyewear. This was to avoid exposure to cholesterol, streptomycin, acrylamide, and TEMED. Acrylamide was obtained and dissolved in water to reduce the risk of acrylamide inhalation. GelRed was used to stain PCR reactions as a safer alternative to ethidium bromide. Ultraviolet exposure was avoided by imaging gels using a gel documentation system. Bacteria and chemical reagents were properly contained and disposed of in the appropriate biohazard waste containers within the laboratory. Bacterial cultures were disposed of following bleaching (10% bleach solution). Bacterial and nematode plates were disposed of following autoclaving. Students were instructed to tie back long hair and loose clothing to avoid safety risk from alcohol burner flame. Students disinfected their bench space before and after each experiment and cleansed their hands before and after each experiment with soap and water or an alcohol-based hand sanitizer. Due to institutional guidelines for the COVID-19 pandemic, students were required to wear a mask or face covering (covering mouth and nose) when inside campus buildings regardless of distancing. For the last 5 weeks of the Spring 2022 semester, students could choose to mask based on personal preference.

We surveyed students following the research symposium to obtain their views on the value of the experimental tasks and activities that were performed during the course and their overall learning experience. We used two questions to obtain a general idea of each student’s experience, specifically the most challenging and rewarding parts of the course that were adapted from a previous instrument (28). Student surveys were analyzed to identify the main themes that emerged, and responses were assigned to each theme. When examining the students’ perceived rewards and challenges of the course, we report the top four themes that were reported by the students across the four semesters (Table 4). Students highlighted an array of rewards and challenges of the course.

All students (100%) who completed the questionnaire shared reward(s) from their experience in the GENE-CURE (Table 4). Many students (82.8%) highlighted that they found learning the process of research to be the most rewarding part of the course. Some students shared that this was their first exposure to scientific research and that they were fortunate to gain this research experience as undergraduate students. Students described learning the process of research and their experience in the GENE-CURE prepared them for future science courses and endeavors in research. Another top student-perceived reward was seeing hard work payoff and their research project progress across the course (70.3%). Students described being intrinsically satisfied with observing their self-generated results and project progress. In line with previous research, the GENE-CURE also observed notable advancements in students’ scientific identity and emotional connection to research when engaging in data analysis within a CURE (29). Additionally, increasing self-confidence in research and gaining an identity as a scientist were mentioned by several students as the most rewarding (28.9%). Notably, numerous students (35.9%) shared that having a personal interest and/or connection to their selected research topic made their own scientific research the most rewarding part of the course. This indicates a potential connection between personal interest and students’ ownership of their research projects. We suspect that students who select their research topic based on a personal connection to the disease may feel more emotional or cognitive ownership toward the overall research project. These hypotheses need to be further explored in future research. Supporting previous findings, this underscores the positive influence of engaging students in meaningful discoveries on their sense of project ownership and academic engagement (30).

The top student-perceived challenge related directly to one of the features of a CURE, the opportunity for students to make discoveries and engage in iterative research (Table 4). Students (41.4%) described being frustrated and overwhelmed with dealing with failure during their research project. Numerous students shared that they were able to troubleshoot and work through a negative result or roadblock with persistence and support from their research group members and instruction team. Examples such as these illustrate that students were able to work through their challenges and failures. The next two student-perceived challenges relate to student struggle with time management (34.4%) and learning new tools and research (21.1%). While these features were reported to be challenging, there were numerous students who added that this experience improved their time management skills and ability to learn new tools and conduct research. Particularly, some students (13.2%) shared struggles with life situations, including issues related to the COVID-19 pandemic. These ranged from students having issues staying focused and on-task in the course to hurdles associated specifically with COVID-19 quarantine and infection. Importantly, numerous students described the resources and support they utilized to overcome these challenges to succeed. In congruence with previous findings, these observations align with the understanding that students can derive valuable benefits from participating in a CURE, even if they do not meet predetermined research objectives (31).

The assessments were designed to critically evaluate the mastery of SLOs and student research progress, ensuring a comprehensive evaluation of students’ understanding and skills. Multiple formative and summative assessments were designed to measure student learning across SLOs and examine the effectiveness of the GENE-CURE (Table 3). The ELN assignment helps guide and support students in experiment documentation and data collection and analysis and is evaluated three times across the course (initial, middle, and final). The project report assignment introduces students to scientific writing through scaffolding and revision and is evaluated twice across the course (initial and final).

Most students showed learning gains across assessments by applying the scientific method to test a hypothesis-driven question and revising science writing. For SLO-1, the assessment data reveal that students effectively applied principles of modern genetic analysis during research projects while recording generated data and maintaining ELNs (Fig. 2A; Appendix 6). Both the ELN and the project report assessment score means were significantly higher from the initial to the final student evaluations (Fig. 2). The mean of differences between the ELN assessment scores was 4.248 (Fig. 2A). A total of 112 out of 125 students (90%) improved their performance from the initial to the final ELN evaluation.

For SLO-3, the assessment data affirm the students’ competence in utilizing the scientific method effectively, as evidenced by their ELNs and project reports, wherein they tested hypothesis-driven questions (Fig. 2A and B; Appendix 6). Additionally, for SLO-4, the assessment data provide clear evidence of students’ ability to revise and enhance their science writing skills within their project reports (Fig. 2B). The mean of differences between the project report assessment scores was 4.170 (Fig. 2B). A total of 100 out of 121 students (83%) improved their performance from the initial to the final project report evaluation. For SLO-5, students reported on individual and group findings through effective preparation and presentation of group posters, and their poster presentations and active involvement in this process demonstrate their achievement (Appendix 6).

RCR education is key to helping trainees create a solid scientific foundation and to improving research integrity (32). Due to the nature of CUREs, it is crucial for students to be introduced to scientific research and RCR, including authorship (33–35). In numerous instances, a CURE is a student’s first exposure to and experience with scientific research (36). Module content and activities were specifically designed to introduce students to these topics during their training and research in the GENE-CURE. For SLO-2, students engaged in training focused on RCR and their active participation and successful completion of the training demonstrate their understanding and assessment of RCR issues in the context of science and scientific research.

The diverse nature of teaching ecosystems should be considered when planning to implement a CURE, including the GENE-CURE curriculum. This highlights the need to consider various educational contexts and the potential variations that may affect the applicability of the study’s framework in different educational settings. Specific factors encompass variations in educational institutions, curriculum structures, student demographics, and available resources. We emphasize the importance of recognizing and understanding these factors when considering the implementation of the framework. To facilitate effective implementation, we provide insights into potential adaptations or modifications needed to tailor the framework to different educational settings. These adaptations may involve adjusting the curriculum to align with specific SLOs for a course, customizing teaching strategies based on student demographics, and considering available resources and technological support.

Numerous modifications are possible depending on the SLOs, research outcomes, and course sequencing. As such, alternative experimental methods can be employed to introduce different scientific skills. For example, the bioinformatic experimentation module can be expanded to include protein modeling experiments to examine the potential structural impacts of VUS on human and/or nematode proteins. A modified version of this GENE-CURE was executed for an undergraduate bioinformatic course (8 students) and a graduate genetics course (15 students), with a focus on assessing the potential structural impact of identified VUS through protein modeling.

Depending on student progress and course sequencing, there are a few experimental tasks that can be modified for student enrichment or with instructor support. For example, students can design their oligonucleotides to move into the “wet lab” sessions. However, if students are slower to progress to a conserved VUS locus, the instructor can design oligonucleotides for students to advance into these experiments quickly. Also, students who advance their projects beyond the genotyping assay can be given the opportunity to design an RNA guide for CRISPR-Cas9 targeting of the VUS region in C. elegans.

Just as with scientific research, the GENE-CURE will evolve with students’ discoveries as conclusions are drawn and new questions emerge. In the coming year, it will transition to allow future students to generate CRISPR-Cas9-engineered C. elegans VUS models based on previous students’ findings. This will allow for further investigation of VUS models with in vivo functional assays to decipher significance. The GENE-CURE has also spurred independent research projects and fostered mentored research allowing students to continue exploring their research question and gain a broader exposure to scientific research.