Course-based Undergraduate Research Experiences Research Articles

Course-Based Undergraduate Research Experiences Performance Following the Transition to Remote Learning During the COVID-19 Pandemic

Course-Based Undergraduate Research Experiences Performance Following the Transition to Remote Learning During the COVID-19 Pandemic

An Approach to Transitioning Undergraduate Biochemistry Laboratory Courses Online

An Approach to Transitioning Undergraduate Biochemistry Laboratory Courses Online

A Course-Based Undergraduate Research Experience in CRISPR-Cas9 Experimental Design to Support Reverse Genetic Studies in Arabidopsis thaliana.

ABSTRACTGene-editing tools such as CRISPR-Cas9 have created unprecedented opportunities for genetic studies in plants and animals. We designed a course-based undergraduate research experience (CURE) to train introductory biology students in the concepts and implementation of gene-editing technology as well as develop their soft skills in data management and scientific communication. We present two versions of the course that can be implemented with twice-weekly meetings over a 5-week period. In the remote-learning version, students performed homology searches, designed guide RNAs (gRNAs) and primers, and learned the principles of molecular cloning. This version is appropriate when access to laboratory equipment or in-person instruction is limited, such as during closures that have occurred in response to the COVID-19 pandemic. In person, students designed gRNAs, cloned CRISPR-Cas9 constructs, and performed genetic transformation of Arabidopsis thaliana. Students learned how to design effective gRNA pairs targeting their assigned gene with an 86% success rate. Final exams tested students’ ability to apply knowledge of an unfamiliar genome database to characterize gene structure and to properly design gRNAs. Average final exam scores of ∼73% and ∼84% for in-person and remote-learning CUREs, respectively, indicated that students met learning outcomes. The highly parallel nature of the CURE makes it possible to target dozens to hundreds of genes, depending on the number of sections. Applying this approach in a sensitized mutant background enables focused reverse genetic screens for genetic suppressors or enhancers. The course can be adapted readily to other organisms or projects that employ gene editing.

Agar Art: a CURE for the Microbiology Laboratory.

ABSTRACTWe previously developed and assessed “The Art of Microbiology,” a course-based undergraduate research experience (CURE) which uses agar art to spur student experimentation, where we found student outcomes related to science persistence. However, these outcomes were not correlated with specific activities and gains were not reported from more than one class. In this study, we explored which of the three major activities in this CURE—agar art, experimental design, or poster presentations—affected student engagement and outcomes associated with improved understanding of the nature of science (NOS). The Art of Microbiology was studied in three microbiology teaching laboratories: at a research university with either the CURE developer (18 students) or a CURE implementer (39 students) and at a community college with a CURE implementer (25 students). Our quasi-experimental mixed methods study used pre/post-NOS surveys and semi-structured class-wide interviews. Community college students had lower baseline NOS responses but had gains in NOS similar to research university students post-CURE. We surveyed research university students following each major activity using the Assessing Student Perspective of Engagement in Class Tool (ASPECT) survey but did not find a correlation between NOS and activity engagement. Of the three activities, we found the highest engagement with agar art, especially in the CURE developer class. Interviewed students in all classes described agar art as a fun, relevant, and low-stakes assignment. This work contributes to the evidence supporting agar art as a curricular tool, especially in ways that can add research to classrooms in and beyond the research university.

Introducing undergraduate students to single-crystal X-ray diffraction through a course-based undergraduate research experience

Introducing undergraduate students to single-crystal X-ray diffraction through a course-based undergraduate research experience

Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students.

About 10% of human proteins have no annotated function in protein knowledge bases. A workflow to generate hypotheses for the function of these uncharacterized proteins has been developed, based on predicted and experimental information on protein properties, interactions, tissular expression, subcellular localization, conservation in other organisms, as well as phenotypic data in mutant model organisms. This workflow has been applied to seven uncharacterized human proteins (C6orf118, C7orf25, CXorf58, RSRP1, SMLR1, TMEM53 and TMEM232) in the frame of a course-based undergraduate research experience named Functionathon organized at the University of Geneva to teach undergraduate students how to use biological databases and bioinformatics tools and interpret the results. C6orf118, CXorf58 and TMEM232 were proposed to be involved in cilia-related functions; TMEM53 and SMLR1 were proposed to be involved in lipid metabolism and C7orf25 and RSRP1 were proposed to be involved in RNA metabolism and gene expression. Experimental strategies to test these hypotheses were also discussed. The results of this manual data mining study may contribute to the project recently launched by the Human Proteome Organization (HUPO) Human Proteome Project aiming to fill gaps in the functional annotation of human proteins.Database URL: http://www.nextprot.org

Student Outcomes From a Large-Enrollment Introductory Course-Based Undergraduate Research Experience on Soil Microbiomes.

In recent years, national reports have called for undergraduate laboratory education that engages students in authentic research experiences. As a result, a number of course-based undergraduate research experiences (CUREs) have been developed in biological sciences and some specifically in microbiology. Students benefit from CUREs much like in traditional mentored research experiences, where students carry out independent projects in faculty laboratories. These benefits include increased self-efficacy in research skills, enhanced identification as scientists, and higher graduation rates in science, technology, engineering, and mathematics majors. Because mentored research experiences are not readily available to every student, CUREs represent a potential mechanism to democratize the research experience by providing such opportunities to all students. However, many of existing CUREs described in the literature are designed for advanced undergraduates or are limited to a small number of students. Here, we report student outcomes from a large-enrollment introductory CURE on soil microbiomes that engages students in a real-world context with microbiology. In pre- and post-course surveys, students reported significant gains in self-efficacy on a number of research skills. These results are triangulated with post-course survey data on project ownership, sense of community, and CURE design elements such as collaboration, iteration, discovery, and relevance.

A novel undergraduate biomedical laboratory course concept in synergy with ongoing faculty research.

Optimal integration of education and ongoing faculty research in many undergraduate science programs is limited to the capstone project. Here, we aimed to develop a novel course‐based undergraduate research experience (CURE) in synergy with ongoing faculty research. This 10‐week course called Biomedical Research Lab is embedded in the curriculum of the undergraduate program Biomedical Sciences and grounded in the theoretical framework of research‐based learning. Four groups of four students work together in a dedicated laboratory on an actual ongoing research problem of faculty. All groups work on the same research problem, albeit from different (methodological) perspectives, thereby stimulating interdependence between all participants. Students propose new research, execute the experiments, and collectively report in a single research article. According to students, the course enhanced scientific, laboratory, and academic skills. Students appreciated ownership and responsibilities of the research, laboratory teachers as role models, and they were inspired and motivated by doing authentic actual research. The course resulted in a better understanding of what doing research entails. Faculty valued the didactical experience, research output and scouting opportunities. Since topics can change per course edition, we have showcased a widely applicable pedagogy creating synergy between ongoing research and undergraduate education.

Connected While Distant: Networking CUREs Across Classrooms to Create Community and Empower Students.

Connections, collaborations, and community are key to the success of individual scientists as well as transformative scientific advances. Intentionally building these components into science, technology, engineering and mathematics (STEM) education can better prepare future generations of researchers. Course-based undergraduate research experiences (CUREs) are a new, fast-growing teaching practice in STEM that expand opportunities for undergraduate students to gain research skills. Because they engage all students in a course in an authentic research experience focused on a relevant scientific problem, CUREs provide an opportunity to foster community among students while promoting critical thinking skills and positively influencing their identities as scientists. Here, we review CUREs in the biological sciences that were developed as multi-institutional networks, and highlight the benefits gained by students and instructors through participation in a CURE network. Throughout, we introduce Squirrel-Net, a network of ecology-focused and field-based CUREs that intentionally create connections among students and instructors. Squirrel-Net CUREs can also be scaffolded into the curriculum to form connections between courses, and are easily transitioned to distance-based delivery. Future assessments of networked CUREs like Squirrel-Net will help elucidate how CURE networks create community and how a cultivated research community impacts students' performance, perceptions of science, and sense of belonging. We hypothesize networked CUREs have the potential to create a broader sense of belonging among students and instructors alike, which could result in better science and more confident scientists.

Bridging Trade-Offs between Traditional and Course-Based Undergraduate Research Experiences by Building Student Communication Skills, Identity, and Interest.

ABSTRACTUndergraduate research plays an important role in the development of science students. The two most common forms of undergraduate research are those in traditional settings (such as internships and research-for-credit in academic research labs) and course-based undergraduate research experiences (CUREs). Both of these settings offer many benefits to students, yet they have unique strengths and weaknesses that lead to trade-offs. Traditional undergraduate research experiences (UREs) offer the benefits of personalized mentorship and experience in a professional setting, which help build students’ professional communication skills, interest, and scientific identity. However, UREs can reach only a limited number of students. On the other end of the trade-off, CUREs offer research authenticity in a many-to-one classroom research environment that reaches more students. CUREs provide real research experience in a collaborative context, but CUREs are not yet necessarily equipping students with all of the experiences needed to transition into a research lab environment outside the classroom. We propose that CURE instructors can bridge trade-offs between UREs and CUREs by deliberately including learning goals and activities in CUREs that recreate the benefits of UREs, specifically in the areas of professional communication, scientific identify, and student interest. To help instructors implement this approach, we provide experience- and evidence-based guidance for student-centered, collaborative learning opportunities.

Stay-on-Task Exercises as a Tool To Maintain Focus during a CRISPR CURE.

ABSTRACTCourse-based undergraduate research experiences (CURE) offer the chance for students to experience authentic research investigation in a classroom setting. Such hands-on experiences afford unique opportunities work on a semi-independent research project in an efficient, structured environment. We have developed a CRISPR CURE in which undergraduate and graduate students use in silico, in vitro, and in vivo techniques to edit a fungal genome. During the development of this course, we have found that the asynchronous nature of the CRISPR CURE activities can be disruptive and lead to unproductive class time. To overcome this challenge, we have developed stay-on-task exercises (SOTEs). These short low-stakes assessments provide structured activities that are performed during these asynchronous incubation periods. SOTE activities leverage potentially unproductive class time and complement the CURE learning objectives. We have found SOTEs to be one method of maintaining classroom structure during a CURE. Furthermore, SOTE complexity, length, and subject can be easily modified to match course learning objectives.

Repetition Is Important to Students and Their Understanding during Laboratory Courses That Include Research.

ABSTRACTCourse-based undergraduate research experiences (CUREs) provide students with opportunities for the same gains that apprenticed research with faculty members offers. As their popularity increases, it is important that critical elements of CUREs be supported by thoughtful design. Student experiences in CUREs can provide important insights into why CUREs are so effective. We present evidence from students who participated in CUREs at the introductory, intermediate, and advanced levels, as well as from graduate teaching assistants for an introductory lab course that included a CURE. Students and teaching assistants describe repetition as a valuable element in CUREs and other laboratory experiences. We used student work and open-ended interviews to identify which of five previously described elements of CUREs students found important. Because repetition was particularly salient, we characterized how students described repetition as they experienced it in courses that contained full-length CUREs or “micro-CUREs.” In prompted interviews, students described how repetition in CUREs provided cognitive (learning concepts) and practical (learning technical skills) value. Recent graduates who had participated in CUREs at each level of their biology education were particularly aware that they placed value on repetition and acknowledged it as motivational in their own learning. Many students described repetition in metacognitive terms, which also suggests that as students advance through laboratory and CURE curricula, their understanding of how repetition supports their learning becomes more sophisticated. Finally, we integrated student descriptions to suggest ways in which repetition can be designed into CUREs or other laboratory courses to support scientific learning and enhance students’ sense of scientific identity.

An Oral Fluorouracil Prodrug, Capecitabine, Mitigates a Gram-Positive Systemic Infection in Mice.

ABSTRACTNew classes of antibiotics are needed to fight bacterial infections, and repurposing existing drugs as antibiotics may enable rapid deployment of new treatments. Screens for antibacterials have been traditionally performed in standard laboratory media, but bacterial pathogens experience very different environmental conditions during infection, including nutrient limitation. To introduce the next generation of researchers to modern drug discovery methods, we developed a course-based undergraduate research experience (CURE) in which undergraduate students screened a library of FDA-approved drugs for their ability, in a nutrient-poor medium, to prevent the growth of the human Gram-negative bacterial pathogen Salmonella enterica serovar Typhimurium. The nine drugs identified all disrupt DNA metabolism in bacteria and eukaryotes. One of the hit compounds, capecitabine, is a well-tolerated oncology drug that is administered orally, a preferred treatment route. We demonstrated that capecitabine is more effective at inhibiting S. Typhimurium growth in nutrient-limited than in standard rich microbiological broth, an explanation for why the antibiotic activity of this compound has not been previously recognized. Capecitabine is enzymatically converted to the active pyrimidine analogue, fluorouracil (5-FU), and Gram-positive bacteria, including Staphylococcus aureus, are significantly more sensitive to 5-FU than Gram-negative bacteria. We therefore tested capecitabine for efficacy in a murine model of S. aureus peritonitis. Oral capecitabine administration reduced the colonization of tissues and increased animal survival in a dose-responsive manner. Since capecitabine is inexpensive, orally available, and relatively safe, it may have utility for treatment of intractable Gram-positive bacterial infections.IMPORTANCE As bacterial infections become increasingly insensitive to antibiotics, whether established, off-patent drugs could treat infections becomes an important question. At the same time, basic research has revealed that during infection, mammals starve pathogens for nutrients and, in response, bacteria dramatically alter their biology. Therefore, it may be fruitful to search for drugs that could be repurposed as antibiotics using bacteria grown with limited nutrients. This approach, executed with undergraduate student researchers, identified nine drugs known to interfere with the production and/or function of DNA. We further explored one of these drugs, capecitabine, a well-tolerated human oncology drug. Oral administration of capecitabine reduced infection with the human pathogen Staphylococcus aureus and increased survival in mice. These data suggest that capecitabine has potential as a therapy for patients with otherwise untreatable bacterial infections.

STUDENT REFLECTIONS IN COURSE-BASED UNDERGRADUATE RESEARCH EXPERIMENT IN A FIRST-YEAR CIRCUITS COURSE

At the University of Calgary, we piloted a course-based undergraduate research experience in thefirst year circuits course. The intention was to provide authentic learning experiences, with the ultimate goal of fostering deep learning in the students. Using qualitative coding, these reflections were analyzed with a framework from self-determination theory to understand the studentlearning and motivation throughout the experience. There were 10 themes that emerged, categorized within the three elements of the theoretical framework: competence, relatedness, and autonomy.

Course-based undergraduate research experiences are a viable approach to increase access to research experiences in biology

ABSTRACT Course-based undergraduate research experiences (CUREs) have been described as a mechanism to allow more undergraduates to engage in research experiences. To understand whether CUREs are viable to scale-up undergraduate access to research experiences, it is essential to carefully evaluate whether CUREs promote comparable self-reported outcomes for students and are less resource intensive than undergraduate research internships. In comparing student outcomes from four distinct CUREs to outcomes from students engaged in a summer research programme in the biology department at one institution, we found that students in both experiences self-report comparable gains on all items studied using the Undergraduate Research Student Self-Assessment tool. CURE students report similar levels of satisfaction with aspects of research experiences, such as amount of time spent conducting research and working with a mentor, compared with students engaged in the summer research programme. The CUREs studied here are less resource intensive than the summer research programme, and still led to comparable self-reported outcomes. These courses increased the number of biology undergraduates able to engage in research experiences, suggesting that CUREs are a viable option to expand access to research experiences that promote expected learning outcomes in a more efficient way.

Incorporating Research into an Undergraduate Animal Behavior Course using Zoos and Webcams.

In our nonmajors animal behavior class, we developed a semester-long research project assignment that incorporates project-based learning (PBL) and the opportunity for Course-Based Undergraduate Research Experiences (CUREs) that introduces, assesses, and applies the course concepts. This project can easily be adapted for nonmajors biology, majors biology, or other more general survey classes, including remote courses. This student-led project involves a field trip for data collection at our local zoo, additional data collection using webcams, and writing and presenting a scientific report. Students apply the scientific method to design their research project and formulate a hypothesis. Throughout the semester, students learn about different behavioral sampling methods and how to develop and use an ethogram in class using animal webcams from zoos. At the zoo, students conduct a comparative behavior project by collecting data from their main animal and two related animals using multiple trials, so students can observe differences in behavior. At the conclusion of the project, students write a report demonstrating their data analysis, graphing, explanation, and interpretation of their own scientific data. We discuss how others can design and implement PBL and CUREs in their classes and what we have learned from our experiences.

Design and Implementation of an Organic to Analytical CURE Sequence

This paper describes the design and implementation of a course-based undergraduate research experience (CURE) sequence in chemistry that links a lower-division, organic chemistry course to an upper-division, analytical chemistry course. The focus of student research is on blood preservation using trehalose derivatives in order to mimic the tardigrade, a microscopic extremophile, which produces sugar molecules to survive desiccation and freezing. Students created a library of modified sugar molecules in the organic CURE and then evaluated the behavior of those molecules within membranes in the analytical CURE. The CURE sequence has been run with three student cohorts which were selected to match the demographics of all students in the course. This article details the student selection process, the course design, the faculty implementation, and revisions. Fidelity of the CURE is demonstrated with survey results. We also describe adaptation of the research courses to accommodate the COVID-19 restrictions.

Students' Perceptions of FSBio 201, A CURE-Based Course that Scaffolds Research and Scientific Communication, Align with Learning Outcomes.

Incorporating active research opportunities into undergraduate curricula is one of the most cited elements demonstrated to improve inclusive excellence and retention in all STEM fields. Allegheny College has a long and nationally-recognized tradition of collaborative student-faculty research within the academic curriculum and as co-curricular opportunities. We present an example of the former, a Course-based Undergraduate Research Experience (CURE), FSBio 201, that has been central to Allegheny’s biology curriculum for over two decades. The course emphasizes biological research design, execution, and communication. We have coded and analyzed feedback from student evaluations and from the national CURE project database, both of which measure students’ perceptions and attitudes toward the course. The majority of the student feedback related to the course learning outcomes of fostering independent research and communication skills was positive. However, we also see areas for improvement, such as how we employ peer-to-peer mentoring and how we teach quantitative and computer-based skills. We conclude that students’ self-reported data are in line with our learning outcomes and provide FSBio 201 as a model for introducing college undergraduates to biological research.

Embedding Research Directly into the Chemistry Curriculum with an Organic to Analytical Sequence

This manuscript describes the implementation of a Course-based Undergraduate Research Experience (CURE) sequence in chemistry that uses research to link a lower division, organic chemistry course to an upper-division, analytical chemistry course. In the CURE sequence, students created a library of modified sugar molecules during CURE-1, Organic, and then evaluated the behavior of those molecules within membranes during CURE-2, Analytical. In order to ascertain the causal mechanisms underlying the effectiveness and sustainability of CUREs within the standard chemistry curriculum, we conducted research on students in CURE laboratories and Standard Instruction (SI) laboratories. Results from the Classroom Undergraduate Research Experience (CURE) Survey, the Laboratory Course Assessment Survey (LCAS), and an end-of-course assessment are presented. Equivalency of the CURE and comparison groups was established based on demographic factors, reported gender and minority status, expected major, and grade in the prerequisite course. A direct comparison of this nature revealed the benefits of the CURE sections and equality in assessment performance regardless of the instructional method.

Postbaccalaureate terminal degree and career choices of students who performed undergraduate research.

This study analyzed terminal degree and career choices of students who performed undergraduate research. In one analysis, the study compared terminal degree and career choices between a course-based undergraduate research experience (CURE) and traditional non-course-based undergraduate research experiences at one primarily undergraduate institution (PUI). Students who pursued postbaccalaureate programs chose terminal degrees at levels exceeding 75%, with no significant difference between a CURE experience and a traditional research experience. Analysis of terminal degree and career choices at four PUIs providing traditional research experiences showed a marked difference in the number of students pursuing terminal degrees. Two PUIs showed rates > 75%, whereas students at the other two PUIs pursued terminal degrees <50% of the time. The majority of students not pursuing terminal degrees chose M.S. degrees in education and healthcare. An analysis was also performed among students participating in traditional summer undergraduate research on a research-intensive university (RIU) campus with a medical school. Students were accepted from two programs, an NIH IDeA Network of Biomedical Research Excellence (INBRE) program recruiting students from the RIU and an NSF Research Experiences for Undergraduates (REU) program recruiting undergraduates from rural PUIs and minority-serving institutions, particularly tribal colleges. Analysis showed that >70% of the students who pursued postbaccalaureate programs chose terminal degrees. INBRE undergraduates displayed a marked preference for the M.D. degree (73.9% vs. 17.4%), whereas the REU students chose the Ph.D. degree (75.0% vs. 22.9%). American Indian students were also analyzed separately for career choice and showed an equal preference for the M.D. and Ph.D. degrees when pursuing postbaccalaureate education. Overall, the results provide evidence that undergraduate student research stimulates student careers in areas needed by the nation's citizen stakeholders.