Supporting the democratization of science during a pandemic: genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy

The initial phase of the COVID-19 pandemic changed the nature of course delivery from largely in-person to exclusively remote, thus disrupting the well-established pedagogy of the Genomics Education Partnership (GEP; https://www.thegep.org). However, our web-based research adapted well to the remote learning environment. As usual, students who engaged in the GEP's Course-based Undergraduate Research Experience (CURE) received digital projects based on genetic information within assembled Drosophila genomes. Adaptations for remote implementation included moving new member faculty training and peer Teaching Assistant office hours from in-person to online. Surprisingly, our faculty membership significantly increased and, hence, the number of supported students. Furthermore, despite the mostly virtual instruction of the 2020-2021 academic year, there was no significant decline in student learning nor attitudes. Based on successfully expanding the GEP CURE within a virtual learning environment, we provide four strategic lessons we infer toward democratizing science education. First, it appears that increasing access to scientific research and professional development opportunities by supporting virtual, cost-free attendance at national conferences attracts more faculty members to educational initiatives. Second, we observed that transitioning new member training to an online platform removed geographical barriers, reducing time and travel demands, and increased access for diverse faculty to join. Third, developing a Virtual Teaching Assistant program increased the availability of peer support, thereby improving the opportunities for student success. Finally, increasing access to web-based technology is critical for providing equitable opportunities for marginalized students to fully participate in research courses. Online CUREs have great potential for democratizing science education.

The Genomics Education Partnership: First findings on genomics research in community colleges

The Genomics Education Partnership (GEP), a consortium of diverse colleges/universities, provides support for integrating genomics research into undergraduate curricula. To increase research opportunities for underrepresented students, GEP is expanding to more community colleges (CC). Genomics research, requiring only a computer with internet access, may be particularly accessible for 2-year institutions with limited research capacity and significant budget constraints. To understand how GEP supports student research at CCs, we analyzed student knowledge and self-reported outcomes. We found that CC student gains are comparable to non-CC student gains, with improvements in attitudes toward science and thriving in science. Our early findings suggest that the GEP model of centralized support with flexible CURE implementation benefits CC students and may help mitigate barriers to implementing research at CCs.

Student Attitudes Contribute to the Effectiveness of a Genomics CURE

The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student's epistemic beliefs to achieving positive learning outcomes.

Connecting research and teaching introductory cell and molecular biology using an Arabidopsis mutant screen

A complex research project was translated into a Course-based Undergraduate Research Experience (CURE), which was implemented in sections of an introductory Cell and Molecular Biology laboratory course. The research laboratory generated an engineered plant line producing a growth-inhibiting, lipid-derived plant hormone and mutagenized this line. Students in the CURE cultured the mutagenized plant population and selected and characterized suppressor mutants. They learned to observe phenotypes related to the biosynthesis and perception of the plant hormone and explored the genetic and biochemical basis of these phenotypes. As the students studied the relevant genetic, molecular and biochemical concepts during this CURE, they were able to translate this knowledge into practice and develop scientific arguments. This CURE was a successful collaboration between the teaching lab and the research lab. It benefited both parties as the students had a real-life, deep learning experience in scientific methodology, while the research lab gathered data and materials for further studies.

A functional genomics screen identifying blood cell development genes in Drosophila by undergraduates participating in a course-based research experience

Undergraduate students participating in the UCLA Undergraduate Research Consortium for Functional Genomics (URCFG) have conducted a two-phased screen using RNA interference (RNAi) in combination with fluorescent reporter proteins to identify genes important for hematopoiesis in Drosophila. This screen disrupted the function of approximately 3500 genes and identified 137 candidate genes for which loss of function leads to observable changes in the hematopoietic development. Targeting RNAi to maturing, progenitor, and regulatory cell types identified key subsets that either limit or promote blood cell maturation. Bioinformatic analysis reveals gene enrichment in several previously uncharacterized areas, including RNA processing and export and vesicular trafficking. Lastly, the participation of students in this course-based undergraduate research experience (CURE) correlated with increased learning gains across several areas, as well as increased STEM retention, indicating that authentic, student-driven research in the form of a CURE represents an impactful and enriching pedagogical approach.

G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation

Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manual gene annotation. This requires access to good genome browsers to enable annotators to visualize and evaluate multiple lines of evidence (e.g., sequence similarity, RNA sequencing [RNA-Seq] results, gene predictions, repeats) and necessitates many volunteers to participate in the work. To address the technical barriers to creating genome browsers, the Genomics Education Partnership (GEP; https://gep.wustl.edu/) has partnered with the Galaxy Project (https://galaxyproject.org) to develop G-OnRamp (http://g-onramp.org), a web-based platform for creating UCSC Genome Browser Assembly Hubs and JBrowse genome browsers. G-OnRamp also converts a JBrowse instance into an Apollo instance for collaborative genome annotations in research and educational settings. The genome browsers produced can be transferred to the CyVerse Data Store for long-term access. G-OnRamp enables researchers to easily visualize their experimental results, educators to create Course-based Undergraduate Research Experiences (CUREs) centered on genome annotation, and students to participate in genomics research. In the process, students learn about genes/genomes and about how to utilize large datasets. Development of G-OnRamp was guided by extensive user feedback. Sixty-five researchers/educators from >40 institutions participated through in-person workshops, which produced >20 genome browsers now available for research and education. Genome browsers generated for four parasitoid wasp species have been used in a CURE engaging students at 15 colleges and universities. Our assessment results in the classroom demonstrate that the genome browsers produced by G-OnRamp are effective tools for engaging undergraduates in research and in enabling their contributions to the scientific literature in genomics. Expansion of such genomics research/education partnerships will be beneficial to researchers, faculty, and students alike.

Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience

A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students' learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our "formative frustration" hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned frustration and struggle, as well as learning and better understanding of the scientific process. Bioinformatics projects are particularly well suited to the process of iteration and refinement because iterations can be performed quickly and are inexpensive in both time and money. Based on these findings, we suggest that a dynamic of "formative frustration" is an important aspect for a successful CURE.

One-Year Research Experience for Associate's Degree Students Impacts Graduation, STEM Retention, and Transfer Patterns

The CUNY Research Scholars Program (CRSP) provides a yearlong faculty-mentored research experience to associate's degree students. The program takes place at all 10 associate's degree-granting colleges within the City University of New York system. We report on a mixed-methods study of 500 students who participated in the program during its initial 3 years. Quantitative longitudinal assessments revealed that students who engaged in CRSP were more likely to be retained in a science, technology, engineering, and mathematics (STEM) discipline or to graduate with a STEM degree than their counterparts in a matched comparison group. Furthermore, students who participated in CRSP demonstrated an increased likelihood of transferring to the more research-intensive 4-year schools within the CUNY system and to R1 universities outside the CUNY system. CRSP students reported an increased sense of belonging in college based on survey data, and focus groups with their mentors provided insight into the factors that led to the gains listed above. These combined results-of student data analysis, student surveys, and mentor focus groups-provide evidence that early research experiences for associate's degree students contribute to their academic success.

Broadening the voice of science: Promoting scientific communication in the undergraduate classroom

Effective and accurate communication of scientific findings is essential. Unfortunately, scientists are not always well trained in how to best communicate their results with other scientists nor do all appreciate the importance of speaking with the public. Here, we provide an example of how the development of oral communication skills can be integrated with research experiences at the undergraduate level. We describe our experiences developing, running, and evaluating a course for undergraduates that complemented their existing undergraduate research experiences with instruction on the nature of science and intensive training on the development of science communication skills. Students delivered science talks, research monologues, and poster presentations about the ecological and evolutionary research in which they were involved. We evaluated the effectiveness of our approach using the CURE survey and a focus group. As expected, undergraduates reported strong benefits to communication skills and confidence. We provide guidance for college researchers, instructors, and administrators interested in motivating and equipping the next generation of scientists to be excellent science communicators.

Teaching broader impacts of science with undergraduate research

Science plays an important role in most aspects of society, and scientists face ethical decisions as a routine part of their work, but science education frequently omits or segregates content related to ethics and broader impacts of science. Undergraduate research experiences have the potential to bridge traditional divides in education and provide a holistic view of science. In practice, these experiences can be inconsistent and may not provide the optimal learning environment. We developed a course that combines seminar and independent research elements to support student learning during undergraduate research, makes ethical and societal impacts of science clear by relating them to the students’ own research projects, and develops students’ ethical decision-making skills. Here, we describe the course and provide resources for developing a similar course.

Students in Fully Online Programs Report More Positive Attitudes toward Science Than Students in Traditional, In-Person Programs

Following the growth of online, higher-education courses, academic institutions are now offering fully online degree programs. Yet it is not clear how students who enroll in fully online degree programs are similar to those students who enroll in in-person ("traditional") degree programs. Because previous work has shown students' attitudes toward science can affect their performance in a course, it is valuable to ask how attitudes toward science differ between these two populations. We studied students who completed a fully online astrobiology course. In an analysis of 451 student responses to the Classroom Undergraduate Research Experience survey, we found online program students began the course with a higher scientific sophistication and a higher sense of personal value of science than those in traditional programs. Precourse attitudes also showed some predictive power of course grades among online students, but not for traditional students. Given established relationships between feelings of personal value, intrinsic motivation, and, in turn, traits such as persistence, our results suggest that open-ended or exploration-based learning may be more engaging to online program students due to their pre-existing attitudes. The converse may also be true, that certain pre-existing attitudes among online program students are more detrimental than they are for traditional program students.

Participation in a Year-Long CURE Embedded into Major Core Genetics and Cellular and Molecular Biology Laboratory Courses Results in Gains in Foundational Biological Concepts and Experimental Design Skills by Novice Undergraduate Researchers

This two-year study describes the assessment of student learning gains arising from participation in a year-long curriculum consisting of a classroom undergraduate research experience (CURE) embedded into second-year, major core Genetics and Cellular and Molecular Biology (CMB) laboratory courses. For the first course in our CURE, students used micro-array or RNAseq analyses to identify genes important for environmental stress responses by Saccharomyces cerevisiae. The students were tasked with creating overexpressing mutants of their genes and designing their own original experiments to investigate the functions of those genes using the overexpression and null mutants in the second CURE course. In order to evaluate student learning gains, we employed three validated concept inventories in a pretest/posttest format and compared gains on the posttest versus the pretest with student laboratory final grades. Our results demonstrated that there was a significant correlation between students earning lower grades in the Genetics laboratory for both years of this study and gains on the Genetics Concept Assessment (GCA). We also demonstrated a correlation between students earning lower grades in the Genetics laboratory and gains on the Introductory Molecular and Cell Biology Assessment (IMCA) for year 1 of the study. Students furthermore demonstrated significant gains in identifying the variable properties of experimental subjects when assessed using the Rubric for Experimental (RED) design tool. Results from the administration of the CURE survey support these findings. Our results suggest that a year-long CURE enables lower performing students to experience greater gains in their foundational skills for success in the STEM disciplines.

Scaling Up: Adapting a Phage-Hunting Course to Increase Participation of First-Year Students in Research

Authentic research experiences are valuable components of effective undergraduate education. Research experiences during the first years of college are especially critical to increase persistence in science, technology, engineering, and mathematics fields. The Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) model provides a high-impact research experience to first-year students but is usually available to a limited number of students, and its implementation is costly in faculty time and laboratory space. To offer a research experience to all students taking introductory biology at Gonzaga University (n = 350/yr), we modified the traditional two-semester SEA-PHAGES course by streamlining the first-semester Phage Discovery lab and integrating the second SEA-PHAGES semester into other courses in the biology curriculum. Because most students in the introductory course are not biology majors, the Phage Discovery semester may be their only encounter with research. To discover whether students benefit from the first semester alone, we assessed the effects of the one-semester Phage Discovery course on students' understanding of course content. Specifically, students showed improvement in knowledge of bacteriophages, lab math skills, and understanding experimental design and interpretation. They also reported learning gains and benefits comparable with other course-based research experiences. Responses to open-ended questions suggest that students experienced this course as a true undergraduate research experience.

Situating Second-Year Success: Understanding Second-Year STEM Experiences at a Liberal Arts College

Challenges particular to second-year students have been identified that can impact persistence in science, technology, engineering, and mathematics (STEM) fields. We implemented a program to improve student success in intermediate-level science courses by helping students to feel they belonged and could succeed in STEM. We used survey measures of perceptions and attitudes and then qualitative measures to characterize the impact of support strategies, including peer mentoring, a second-year science student retreat, learning and advising support resources, and department-specific activities. Analysis of registration and transcript information revealed underperformance by students of color (SOC) and first-generation (FG) students in 200-level science courses. Comparison of these data before and during programming revealed significant improvement in success rates of these students in 200-level biology and chemistry courses, but success rates of SOC and FG students remain lower than the overall rate for 200-level science courses. Contemporaneous with the program, qualitative and quantitative measures of student attitudes revealed a high level of belongingness and support. The results suggest that a focus on students' metacognition about their own abilities and strategic knowledge of how to succeed may be a fruitful direction for future research.

A broadly implementable research course in phage discovery and genomics for first-year undergraduate students

Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students' interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training.

IMPORTANCE

Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.

A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics

In their 2012 report, the President's Council of Advisors on Science and Technology advocated "replacing standard science laboratory courses with discovery-based research courses"-a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates.

A course-based research experience: how benefits change with increased investment in instructional time

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

The C.R.E.A.T.E. approach to primary literature shifts undergraduates' self-assessed ability to read and analyze journal articles, attitudes about science, and epistemological beliefs

The C.R.E.A.T.E. (Consider, Read, Elucidate hypotheses, Analyze and interpret data, Think of the next Experiment) method uses intensive analysis of primary literature in the undergraduate classroom to demystify and humanize science. We have reported previously that the method improves students' critical thinking and content integration abilities, while at the same time enhancing their self-reported understanding of "who does science, and why." We report here the results of an assessment that addressed C.R.E.A.T.E. students' attitudes about the nature of science, beliefs about learning, and confidence in their ability to read, analyze, and explain research articles. Using a Likert-style survey administered pre- and postcourse, we found significant changes in students' confidence in their ability to read and analyze primary literature, self-assessed understanding of the nature of science, and epistemological beliefs (e.g., their sense of whether knowledge is certain and scientific talent innate). Thus, within a single semester, the inexpensive C.R.E.A.T.E. method can shift not just students' analytical abilities and understanding of scientists as people, but can also positively affect students' confidence with analysis of primary literature, their insight into the processes of science, and their beliefs about learning.

Classroom-based science research at the introductory level: changes in career choices and attitude

Our study, focused on classroom-based research at the introductory level and using the Phage Genomics course as the model, shows evidence that first-year students doing research learn the process of science as well as how scientists practice science. A preliminary but notable outcome of our work, which is based on a small sample, is the change in student interest in considering different career choices such as graduate education and science in general. This is particularly notable, as previous research has described research internships as clarifying or confirming rather than changing undergraduates' decisions to pursue graduate education. We hypothesize that our results differ from previous studies of the impact of engaging in research because the students in our study are still in the early stages of their undergraduate careers. Our work builds upon the classroom-based research movement and should be viewed as encouraging to the Vision and Change in Undergraduate Biology Education movement advocated by the American Association for the Advancement of Science, the National Science Foundation, and other undergraduate education stakeholders.

Contributions of elicitation to measures of self-control

Pigeons' not pecking or pecking constituted choice between a delayed, large reinforcer and an immediate, small reinforcer (self-control) and at other times between a delayed reinforcer and no reinforcer (omission). Both a tone and a keylight were tested as choice signals, and the delayed reinforcer was either response independent or response dependent. Pigeons pecked during the choice signals on over 95% of the trials in the self-control procedure, and pecked during the choice signals on over 75% of the trials in the omission procedure. Consistent pecking was observed with either the tone or the keylight as a choice signal, with the exception that a tone paired with a response-independent delayed reinforcer did not maintain pecking in the omission procedure. Pigeons pecked during more choice signals when delayed reinforcers were response dependent than when the delayed reinforcers were response independent. These results indicate that Pavlovian conditioning influences self-control experiments, especially in single-key procedures.

The genomics education partnership: successful integration of research into laboratory classes at a diverse group of undergraduate institutions

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.

"Deconstructing" scientific research: a practical and scalable pedagogical tool to provide evidence-based science instruction

Focused analysis of current research projects provides an effective platform for teaching early-stage undergraduates the logic of scientific inquiry.

Undergraduate research. Genomics Education Partnership

The Genomics Education Partnership offers an inclusive model for undergraduate research experiences incorporated into the academic year science curriculum, with students pooling their work to contribute to international data bases.

Undergraduate research. Genomics Education Partnership

The Genomics Education Partnership offers an inclusive model for undergraduate research experiences incorporated into the academic year science curriculum, with students pooling their work to contribute to international data bases.

Undergraduate research experiences support science career decisions and active learning

The present study examined the reliability of student evaluations of summer undergraduate research experiences using the SURE (Survey of Undergraduate Research Experiences) and a follow-up survey disseminated 9 mo later. The survey further examines the hypothesis that undergraduate research enhances the educational experience of science undergraduates, attracts and retains talented students to careers in science, and acts as a pathway for minority students into science careers. Undergraduates participated in an online survey on the benefits of undergraduate research experiences. Participants indicated gains on 20 potential benefits and reported on career plans. Most of the participants began or continued to plan for postgraduate education in the sciences. A small group of students who discontinued their plans for postgraduate science education reported significantly lower gains than continuing students. Women and men reported similar levels of benefits and similar patterns of career plans. Undergraduate researchers from underrepresented groups reported higher learning gains than comparison students. The results replicated previously reported data from this survey. The follow-up survey indicated that students reported gains in independence, intrinsic motivation to learn, and active participation in courses taken after the summer undergraduate research experience.

Keypecking as a Self-Control Response

Self-control was analyzed in an operant conditioning experiment using pigeons as subjects. In past experiments, subjects were presented a brief stimulus such that a peck against a response key during the stimulus resulted in a small reinforcer, and not pecking during the stimulus resulted in a large reinforcer, delivered sometime later. Pecking the response key represented a lack of self-control; not keypecking represented self-control. Because evidence shows a stimulus that precedes a reinforcer can elicit keypecking, and possibly complicate the analysis of the self-control, we changed the self-control response. We made keypecking the response that led to the large reinforcer, and we made not keypecking the response that led to the small reinforcer. This change greatly improved self-control as compared to previous experiments. It also illustrated the fact that many elicited responses were probably present in previous self-control experiments.