Fear of the CURE: A Beginner's Guide to Overcoming Barriers in Creating a Course-Based Undergraduate Research Experience

A plant mutant screen CURE integrated with core biology concepts showed effectiveness in course design and students' perceived learning gains

Course-based undergraduate research experiences (CUREs) provide students with valuable opportunities to engage in research in a classroom setting, expanding access to research opportunities for undergraduates, fostering inclusive research and learning environments, and bridging the gap between the research and education communities. While scientific practices, integral to the scientific discovery process, have been widely implemented in CUREs, there have been relatively few reports emphasizing the incorporation of core biology concepts into CURE curricula. In this study, we present a CURE that integrates core biology concepts, including genetic information flow, phenotype-genotype relationships, mutations and mutants, and structure-function relationships, within the context of mutant screening and gene loci identification. The design of this laboratory course aligns with key CURE criteria, as demonstrated by data collected through the laboratory course assessment survey (LCAS). The survey of undergraduate research experiences (SURE) demonstrates students' learning gains in both course-directed skills and transferrable skills following their participation in the CURE. Additionally, concept survey data reflect students' self-perceived understanding of the aforementioned core biological concepts. Given that genetic mutant screens are central to the study of gene function in biology, we anticipate that this CURE holds potential value for educators and researchers who are interested in designing and implementing a mutant screen CURE in their classrooms. This can be accomplished through independent research or by establishing partnerships between different units or institutions.

Dipping Your Toe in The CURE Pool: Longitudinal Tracking of Instructors Suggests Use of a Short-Duration CURE Can Catalyze Expansion to Longer CURE Experiences

Course-based undergraduate research experiences (CUREs) are an effective method of engaging large numbers of students in authentic research but are associated with barriers to adoption. Short CURE modules may serve as a low-barrier entryway, but their effectiveness in promoting expansion has not been studied. The Prevalence of Antibiotic Resistance in the Environment (PARE) project is a modular CURE designed to be a low-barrier gateway into CURE use. In a series of interviews, we track and characterize use of PARE in 19 PARE-interested instructors throughout the Innovation-Decision Process described by Rogers' Diffusion of Innovations theory. The majority (16/19) implement PARE at least once, and a majority of these implementers (11/16) expanded use by the final interview. Three of four cases of discontinuance were due to a disruption such as moving institutions or a change in course assignment and occurred for community college faculty. Expanders expressed fewer personal challenges than nonexpanders. Overall analysis shows that perception of barriers is nuanced and impacted by the innovation itself, the institutional context, and one's own experiences. These results suggest that a short duration, low barrier CURE can serve as a catalyst for implementation of a longer duration CURE.

Characterization of the Structural Requirements for the NADase Activity of Bacterial Toll/IL-1R domains in a Course-based Undergraduate Research Experience

TLRs initiate innate immune signaling pathways via Toll/IL-1R (TIR) domains on their cytoplasmic tails. Various bacterial species also express TIR domain-containing proteins that contribute to bacterial evasion of the innate immune system. Bacterial TIR domains, along with the mammalian sterile α and TIR motif-containing protein 1 and TIRs from plants, also have been found to exhibit NADase activity. Initial X-ray crystallographic studies of the bacterial TIR from Acinetobacter baumannii provided insight into bacterial TIR structure but were unsuccessful in cocrystallization with the NAD+ ligand, leading to further questions about the TIR NAD binding site. In this study, we designed a Course-Based Undergraduate Research Experience (CURE) involving 16-20 students per year to identify amino acids crucial for NADase activity of A. baumannii TIR domain protein and the TIR from Escherichia coli (TIR domain-containing protein C). Students used structural data to identify amino acids that they hypothesized would play a role in TIR NADase activity, and created plasmids to express mutated TIRs through site-directed mutagenesis. Mutant TIRs were expressed, purified, and tested for NADase activity. The results from these studies provide evidence for a conformational change upon NAD binding, as was predicted by recent cryogenic electron microscopy and hydrogen-deuterium exchange mass spectrometry studies. Along with corroborating recent characterization of TIR NADases that could contribute to drug development for diseases associated with dysregulated TIR activity, this work also highlights the value of CURE-based projects for inclusion of a diverse group of students in authentic research experiences.

CURE on yeast genes of unknown function increases students' bioinformatics proficiency and research confidence

Course-based undergraduate research experiences (CUREs) can reduce barriers to research opportunities while increasing student knowledge and confidence. However, the number of widely adopted, easily transferable CUREs is relatively small. Here, we describe a CURE aimed at determining the function of poorly characterized Saccharomyces cerevisiae genes. More than 20 years after sequencing of the yeast genome, nearly 10% of open reading frames (ORFs) still have at least one uncharacterized Gene Ontology (GO) term. We refer to these genes as "ORFans" and formed a consortium aimed at assigning functions to them. Specifically, over 70 faculty members attended summer workshops to learn the bioinformatics workflow and basic laboratory techniques described herein. Ultimately, this CURE was adapted for implementation at 34 institutions, resulting in over 1,300 students conducting course-based research on ORFans. Pre-/post-tests confirmed that students gained both (i) an understanding of gene ontology and (ii) knowledge regarding the use of bioinformatics to assign gene function. After using these data to craft their own hypotheses, then testing their predictions by constructing and phenotyping deletion strains, students self-reported significant gains in several areas, including computer modeling and exposure to a project where no one knows the outcome. Interestingly, most net gains self-reported by ORFan Gene Project participants were greater than published findings for CUREs assessed with the same survey instrument. The surprisingly strong impact of this CURE may be due to the incoming lack of experience of ORFan Project participants and/or the independent thought required to develop testable hypotheses from complex data sets.

A framework for leveraging network course-based undergraduate research experience (CURE) faculty to develop, validate, and administer an assessment instrument

Over the last several years, nationally disseminated course-based undergraduate research experiences (CUREs) have emerged as an alternative to developing a novel CURE from scratch, but objective assessment of these multi-institution (network) CUREs across institutions is challenging due to differences in student populations, instructors, and fidelity of implementation. The time, money, and skills required to develop and validate a CURE-specific assessment instrument can be prohibitive. Here, we describe a co-design process for assessing a network CURE [the Prevalence of Antibiotic Resistance in the Environment (PARE)] that did not require support through external funding, was a relatively low time commitment for participating instructors, and resulted in a validated instrument that is usable across diverse PARE network institution types and implementation styles. Data collection efforts have involved over two dozen unique institutions, 42 course offerings, and over 1,300 pre-/post-matched assessment record data points. We demonstrated significant student learning gains but with small effect size in both content and science process skills after participation in the two laboratory sessions associated with the core PARE module. These results show promise for the efficacy of short-duration CUREs, an educational research area ripe for further investigation, and may support efforts to lower barriers for instructor adoption by leveraging a CURE network for developing and validating assessment tools.

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

Genetic analysis in model systems using bioinformatic approaches provides a rich context for a concrete and conceptual understanding of gene structure and function. With the intent to engage students in research and explore disease biology utilizing the nematode Caenorhabditis elegans model, we developed a semester-long course-based undergraduate research experience (CURE) in a hybrid (online/in-person) learning environment-the gene-editing and evolutionary nematode exploration CURE (GENE-CURE). Using a combination of bioinformatic and molecular genetic tools, students performed structure-function analysis of disease-associated variants of uncertain significance (VUS) in human orthologs. With the aid of a series of workshop-style research sessions, students worked in teams of two to six members to identify a conserved VUS locus across species and design and test a polymerase chain reaction-based assay for targeted editing of a gene in the nematode and downstream genotyping. Research session discussions, responsible conduct of research training, electronic laboratory notebook, project reports, quizzes, and group poster presentations at a research symposium were assessed for mastery of learning objectives and research progress. Self-reflections were collected from students to assess engagement, science identity, and science efficacy. Qualitative analysis of these reflections indicated several gains suggesting that all students found many aspects of the GENE-CURE rewarding (learning process of research, self-confidence in research and science identity, and personal interest) and challenging (iterative research and failure, time management, COVID-19 pandemic, and life issues).

Developing scientific literacy with a cyclic independent study assisted CURE detecting SARS-CoV-2 in wastewater

The COVID-19 pandemic has exposed a high level of scientific illiteracy and mistrust that pervades the scientific and medical communities. This finding has proven the necessity of updating current methods used to expose undergraduates to research. The research in traditional course-based undergraduate research experiences (CUREs) is limited by undergraduate time constraints, skill level, and course structure, and consequently it does not attain the learning objectives or the high-impact, relevant studies achieved in graduate-level laboratories using a cyclic trainee/trainer model. Although undergraduate independent study (ISY) research more closely matches the structure and learning objectives of graduate-level research, they are uncommon as professors and universities typically view them as a significant time and resource burden with limited return. Cyclic independent study-assisted CUREs (CIS-CUREs) combine many positive aspects of ISY graduate-level research, and CUREs by pre-training ISY research lead to facilitate CURE proposal and project semesters in a cyclic model. The CIS-CURE approach allowed undergraduate students at Stetson University to perform and disseminate more rigorous, involved, long-term, and challenging research projects, such as the surveillance of SARS-CoV-2 in wastewater. In doing so, all students would have the opportunity to participate in a high-impact research project and consequently gain a more comprehensive training, reach higher levels of research dissemination, and increase their competitiveness after graduating. Together, CIS-CUREs generate graduates with higher scientific literacy and thus combat scientific mistrust in communities.

Faculty Experiences during the Implementation of an Introductory Biology Course-Based Undergraduate Research Experience (CURE)

Course-based undergraduate research experiences (CUREs) integrate an authentic research experience for students into a laboratory course. CUREs provide many of the same benefits to students as individual faculty-mentored research experiences. However, faculty experiences in teaching CUREs are not as well understood. There are no studies that compare faculty's anticipated experiences to actual experiences, and little comparison of the faculty experience by institution. Through interviews with eight biology faculty from four institutions, the faculty experience in implementing a CURE in an introductory biology laboratory was explored using qualitative analysis. Institutions included: a small, minority-serving, women's, primarily undergraduate university; a small, residential, primarily undergraduate college; a midsized doctoral university; and a large community college. Interviews were conducted at three time points: before professional development (PD), after the initial semester of teaching the CURE, and after teaching the CURE at least twice (1 year later). Faculty described resources, benefits, challenges, and feelings about teaching the CURE. However, anticipated experiences were often not the same as those actually experienced. There were also institutional differences in resources, benefits, challenges, and feelings. Implications for CURE PD include specific content such as strategies for teaching effective research group work, development of student proposals, and student time management.

yEvo: experimental evolution in high school classrooms selects for novel mutations that impact clotrimazole resistance in Saccharomyces cerevisiae

Antifungal resistance in pathogenic fungi is a growing global health concern. Nonpathogenic laboratory strains of Saccharomyces cerevisiae are an important model for studying mechanisms of antifungal resistance that are relevant to understanding the same processes in pathogenic fungi. We have developed a series of laboratory modules in which high school students used experimental evolution to study antifungal resistance by isolating azole-resistant S. cerevisiae mutants and examining the genetic basis of resistance. We have sequenced 99 clones from these experiments and found that all possessed mutations previously shown to impact azole resistance, validating our approach. We additionally found recurrent mutations in an mRNA degradation pathway and an uncharacterized mitochondrial protein (Csf1) that have possible mechanistic connections to azole resistance. The scale of replication in this initiative allowed us to identify candidate epistatic interactions, as evidenced by pairs of mutations that occur in the same clone more frequently than expected by chance (positive epistasis) or less frequently (negative epistasis). We validated one of these pairs, a negative epistatic interaction between gain-of-function mutations in the multidrug resistance transcription factors Pdr1 and Pdr3. This high school-university collaboration can serve as a model for involving members of the broader public in the scientific process to make meaningful discoveries in biomedical research.

The Batrachian Barf Bowl: An authentic research experience using ecological data from frog diets

Authentic research experiences (AREs) are a powerful strategy for inspiring and retaining students in science, technology, engineering, and math (STEM) fields. However, recent demand for virtual learning has emphasized the need for remote AREs that also foster a sense of community and interpersonal connections among participants. Here, we describe an ARE activity that leverages digitized diet data from natural history collections to provide students with collaborative research experience across any learning environment. Using magnified photographs of frog stomach contents collected in the Peruvian Amazon, we designed an open-source "bowl game" competition that challenges students to identify, measure, and compare diet items across vouchered frog specimens ("Batrachian Barf Bowl"). To demonstrate learning outcomes, we ran this activity with 39 herpetology class students from the University of Notre Dame and the University of Michigan. We used pre- and post-activity assessments to evaluate effectiveness, scientific accuracy of results, and impact on student well-being. With minimal preparation and training in invertebrate identification, students were successful in identifying hundreds of frog diet items to taxonomic order, although accuracy varied among clades (global accuracy ~70%). While we found no difference in science identity, community, or self-efficacy between the two institutions at either time point (pre- and post-activity), we found that well-being was significantly higher for both sets of students after the activity. Overall, this approach offers a model for combining active learning with museum collections to provide experiential research opportunities that highlight the power of scientific collaboration.

Real-time text message surveys reveal student perceptions of personnel resources throughout a course-based research experience

Course-based research experiences (CREs) are designed to engage students in authentic scientific experiences that are embedded into a standard curriculum. CREs provide valuable research experiences to large numbers of undergraduate biology students, however, CRE implementation can require many personnel. Because limited personnel may be a barrier to widespread CRE implementation, our goal was to discover which personnel students valued throughout a CRE and the ways they were valuable. We investigated students’ perceptions of personnel resources throughout a semester-long CRE using two survey approaches. Using a text message survey administered multiple times per week, real-time data was collected about which personnel resource students perceived to be the most helpful. Using a web-based survey administered five times throughout the semester, retrospective data was collected about how often students used each personnel resource and how helpful students perceived each personnel resource to be. Graduate teaching assistants (TAs) were consistently selected as the most helpful personnel resource by the majority of respondents throughout the semester, with most respondents describing graduate TAs providing project-specific feedback. Although less frequently, undergraduate TAs were also consistently selected as the most helpful personnel resource. Respondents described undergraduate TAs providing project-specific feedback, general feedback, and project-specific resources. Data from the retrospective, web-based survey largely mirrored the real-time, text message survey data. Throughout the semester, most respondents reported using graduate TAs “Often” or “Always” and that graduate TAs were “Very” or “Extremely” helpful. Throughout most of the semester, most respondents also reported using undergraduate TAs “Often” or “Always” and that undergraduate TAs were “Very” or “Extremely” helpful. The results of this descriptive study underscore the importance of graduate and undergraduate TAs in the development and implementation of CREs, emphasizing the need for departments and course coordinators to be intentional in planning TA training that prepares TAs to fulfill their critical role in CRE implementation.

Antiracist Opportunities in the Journal of Microbiology and Biology Education: Considerations for Diversity, Equity, and Inclusion

Authors in the Journal of Microbiology and Biology Education (JMBE) have demonstrated a clear commitment to diversity, equity, and inclusion (DEI) through commentaries, instructional approaches, and research. However, analysis of JMBE literature using Kendi's antiracist framework (How To Be an Antiracist, 2019) offers additional opportunities for growth. These opportunities are discussed and framed under five emergent conceptual categories (ECCs). First, capitalistic goals (e.g., productivity) are often drivers for DEI initiatives but disproportionately benefit those with power. Humanity-centered reasons, like honoring community values, are also important motivations. Second, faculty are often targeted as primary agents of change for DEI, but more powerful stakeholders such as department and institutional leadership can also implement equitable policies and practices to widen the impact of DEI initiatives. Third, study scopes are sometimes focused on the outcomes of inequity (e.g., lower retention rates for students of color) rather than the systemic causes (e.g., exclusivity of science). While outcomes are important to research, studies should create clear connections and distinctions between the systems and symptoms of inequity. Fourth, active learning and authentic research experiences are not automatically inclusive and do not necessarily validate students' identities. Such approaches may be more impactful when tailored for context and student background. Finally, language and communication can have broad impacts on DEI efforts. As a community, we may need to be more critical of our shared language and communication. This review discusses the five ECCs in depth and offers next steps for supporting DEI across the biology and microbiology education community.

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

Course-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

Course-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.

Building a laboratory at a Primarily Undergraduate Institution (PUI)

Scientists who are interested in building research programs at primarily-undergraduate institutions (PUIs) have unique considerations compared to colleagues at research-intensive (R1) institutions. Maintaining a research program at a PUI holds unique challenges that should be considered before prospective faculty go on the job market, as they negotiate a job offer, and after they begin a new position. In this article we describe some of the considerations that aspiring and newly hired faculty should keep in mind as they plan out how they will set up a laboratory as a new Principle Investigator (PI) at a PUI.Anyone hoping to start a research program at a PUI should understand both the timeframe of interviews, job offers, and negotiations and the challenges and rewards of working with undergraduate researchers. Once a job is offered, candidates should be aware of the range of negotiable terms that can be part of a start-up package. Space and equipment considerations are also important, and making the most of shared spaces, existing infrastructure, and deals can extend the purchasing power of start-up funds as a new PIs builds their lab. PUIs' focus on undergraduate education and mentorship leads to important opportunities for collaboration, funding, and bringing research projects directly into undergraduate teaching laboratories.A major focus of any new laboratory leader must be on building a productive, equitable, and supportive laboratory community. Equitable onboarding, mentorship plans, and formalized expectations, can all help build a productive and sustainable laboratory research program. However, important considerations about safety, inclusion, student schedules, and a PI's own professional commitments are also extremely important concerns when working with undergraduates in research. A successful research program at a PUI will bring students into meaningful scientific inquiry and requires insights and skills that are often not the focus of scientific training. This article aims to describe the scope of setting up a new laboratory as a way to alleviate some of the burden that new and prospective faculty often feel.

Obtaining a faculty position at a primarily undergraduate institution (PUI)

Scientists who hope to obtain a faculty position at a primarily undergraduate institution (PUI) need a distinct skill set and outlook on their future teaching and research career. To obtain a position at a PUI, candidates should 1) design a strategy for obtaining a faculty position that suits each individual’s career goals and aspirations, 2) prepare for the application process, on-campus interview, and contract negotiations, and 3) plan a strategy for the probationary period leading up to tenure and promotion. Given the different types of PUIs, candidates need to consider whether they seek a position that consists of all or mostly all teaching, or both teaching and research. Candidates should educate themselves on the expectations at PUI’s, including current thought, practice, and aspirations for science pedagogy, and gain teaching experience prior to seeking a suitable position. If the candidate’s goal is a position with both teaching and research, it is important to discuss with the current research mentor what projects the candidate can take with them to their new position. The candidate should also consider what types of projects will be successful with undergraduate student researchers in a PUI research environment. Importantly, candidates should clearly demonstrate a commitment to diversity and inclusion in their teaching, research, and outreach, and application materials should demonstrate this. On interviews, candidates should be knowledgeable about the mission, values, and resources of the institution and how the candidate will contribute to that mission. Once hired, new faculty should discuss a formal or informal mentoring plan during the probationary period that includes peer evaluations on a regular basis, and maintain communication with the department chair or designated mentor regarding teaching, research, and service activities.

Is This Science? Students' Experiences of Failure Make a Research-Based Course Feel Authentic

Course-based undergraduate research experiences (CUREs) and inquiry-based curricula both expose students to the scientific process. CUREs additionally engage students in novel and scientifically relevant research, with the intention of providing an "authentic" research experience. However, we have little understanding of which course design elements impact students' beliefs that they are experiencing "authentic" research. We designed a study to explore introductory biology students' perceptions of research authenticity in CURE and inquiry classes. Using the Laboratory Course Assessment Survey, we found that students in CURE sections perceived higher levels of authentic research elements than students in inquiry-based sections. To identify specific factors that impact perceptions of research authenticity, we administered weekly reflection questions to CURE students. Coding of reflection responses revealed that experiences of failure, iteration, using scientific practices, and the relevant discoveries in their projects enhanced students' perceived authenticity of their research experiences. Although failure and iteration can occur in both CUREs and inquiry-based curricula, our findings indicate these experiences-in conjunction with the Relevant Discovery element of a CURE-may be particularly powerful in enhancing student perceptions of research authenticity in a CURE.

Inclusion in neuroscience through high impact courses

Recognizing that STEM disciplines, including neuroscience, have a long way to go to attract and retain diverse talent, educators can take action by being more intentional about their departmental curricula, course design, and pedagogical strategies. A deep body of research suggests that one way we can promote inclusion is through the use of high impact practices (HIPs). These active learning teaching practices promote deep learning and student engagement and have been shown to have a positive differential impact on historically underserved student populations. Here we describe the characteristics of two different types of HIP courses, makerspace classes, and course-based undergraduate research experiences (CUREs). In addition, we provide ideas for how these courses can be structured to help all students engage and learn. With experience overseeing a large campus-wide program introducing these course types to the curriculum, we also provide insights about faculty experiences and assessment. We propose that including these types of courses in a curriculum can engage a more diverse group of students to choose neuroscience as a major and as a career.