Course-based Undergraduate Research Experiences Research Articles

Adapting an Interdisciplinary, Course-Based Undergraduate Research Experience (CURE) Course to an Online Format

August 2020 marked the inaugural CURE Science Bootcamp course. Due to COVID-19 restrictions, the entire bootcamp was taught virtually on a synchronous schedule using the learning management system Blackboard Collaborate Ultra. STEM transfer students completed all key elements of the traditional Science Bootcamp, with slight modifications due to the compressed schedule. In topic selection, students were nudged toward viable methodologies, given that in-person data collection was prohibited.

Assessment of Student Learning in Undergraduate Courses with Collaborative Projects from the Ecological Research as Education Network (EREN)

Multisite, course-based undergraduate research experiences (CUREs) in the Ecological Research as Education Network (EREN) were assessed for impacts on student learning of collaborative science skills using a survey that could serve as a starting point for a validated assessment instrument for multisite CUREs. Pretests/posttests were administered across multiple courses and institutions, capturing effects of diverse EREN projects and pedagogies on collaborative knowledge.

Fermentation revival in the classroom: investigating ancient human practices as CUREs for modern diseases.

A course-based undergraduate research experience (CURE) was designed to integrate key microbiological principles and techniques into an authentic research experience in a classroom setting and was implemented in an undergraduate microbiology laboratory course. Students conducted a 6-week study in order to determine the identity and quantity of unique probiotic species from various types of kefir. This course module followed an inquiry-based pedagogical approach in which students use the scientific process to investigate an unknown question with no predetermined outcome. During each lab, relevant microbiological topics and laboratory concepts were presented. Students then performed various laboratory techniques, reinforcing the lecture material with hands-on experience. In addition, students participated in reflection through group presentation of their results, bioinformatic analysis and literature review. Based on data collected from pre- and post-study survey responses, both student knowledge and attitudes towards the topics covered improved due to participation in this CURE. Importantly, this CURE can be implemented at many levels of education, requiring only minimal resources and common laboratory equipment.

Combining Microbial Culturing With Mathematical Modeling in an Introductory Course-Based Undergraduate Research Experience.

Quantitative techniques are a critical part of contemporary biology research, but students interested in biology enter college with widely varying quantitative skills and attitudes toward mathematics. Course-based undergraduate research experiences (CUREs) may be an early way to build student competency and positive attitudes. Here we describe the design, implementation, and assessment of an introductory quantitative CURE focused on halophilic microbes. In this CURE, students culture and isolate halophilic microbes from environmental and food samples, perform growth assays, then use mathematical modeling to quantify the growth rate of strains in different salinities. To assess how the course may impact students’ future academic plans and attitudes toward the use of math in biology, we used pre- and post-quarter surveys. Students who completed the course showed more positive attitudes toward science learning and an increased interest in pursuing additional quantitative biology experiences. We argue that the classroom application of microbiology methods, combined with mathematical modeling using student-generated data, provides a degree of student ownership, collaboration, iteration, and discovery that makes quantitative learning both relevant and exciting to students.

Participation in a Course-Based Undergraduate Research Experience Results in Higher Grades in the Companion Lecture Course

Opportunities for large numbers of undergraduates to engage in authentic research experiences are limited in many large public institutions. These large public institutions serve the vast majority of students who are historically underrepresented in STEM fields, such as first-generation, low-income students of color. Although a course-based undergraduate research experience (CURE) is one scalable approach to providing such opportunities, there is limited evidence about the impact of participation, particularly for students historically underrepresented in science. This study provides evidence of the influence of student participation in a CURE on undergraduate science course grades using an experimental design and multiple years of data from students at a Hispanic-serving institution. Course grades were compared for five different science courses across five cohorts of students participating in a CURE ( n = 935) and a similar group of students who did not participate in the CURE ( n = 1,144). CURE students had significantly higher overall grades in a lecture course directly related to the CURE even after statistically adjusting for demographic and academic characteristics. Implications for CUREs as a model for improving science knowledge and achievement for students typically underrepresented in STEM fields are discussed.

There're CRISPRs in My Yogurt: A Discovery-Based CURE at the Intersection of Industrial Food Production and the Human Microbiome.

Support for undergraduate laboratory education based on a CURE (Course-based Undergraduate Research Experience) model is more widespread than ever. By giving students the opportunity to conduct genuine research in laboratory courses they are required to take, CUREs can expose more students to scientific practice and have the potential to make science more inclusive, especially when research topics have direct impact on students’ lives. Here, I present a new microbiology CURE module where students explore the real-world intersection between industrial food production and the human microbiome. In this module, students sequence CRISPR arrays in the genomes of lactic acid bacteria they isolate from yogurt. Natural CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) act as the bacterial immune system. When a bacterial cell survives viral infection, it can incorporate a bit of that virus’s DNA into its own genome, and produce small RNA guides that surveil the cell, ready to deploy virus-destroying enzymes if matching DNA from a fresh viral infection is detected. This viral immunity is of particular interest in the fermentation industry, since viral infection can destroy stocks of starter cultures and batches of product. Commercial producers of lactic acid bacteria for yogurt production often endeavor to produce strains with large CRISPR arrays and robust immunities. With this context, students are given the task of cataloging the viral immunities found in both commercial and traditionally produced yogurt, and exploring their potential impact on human health. Wet-lab practices (strain isolation, PCR, and Sanger sequencing) are combined with bioinformatic and literature sleuthing to identify the viruses to which bacteria are immune and explore whether consumption of these strains could impact human health via interactions with the human microbiome. Here, a detailed implementation of the module is presented with guides for educators and students.

The Bean Beetle Microbiome Project: A Course-Based Undergraduate Research Experience in Microbiology

Course-based undergraduate research experiences (CUREs) are an effective means of transforming the learning and teaching of science by involving students in the scientific process. The potential importance of the microbiome in shaping both environmental health and disease makes investigations of microbiomes an excellent teaching tool for undergraduate microbiology. Here, we present a CURE based on the microbiome of the bean beetle (Callosobruchus maculatus), a model system for undergraduate laboratory education. Despite the extensive research literature on bean beetles, little is known about their microbiome, making them an ideal system for a discovery-based CURE. In the CURE, students acquire microbiological technical skills by characterizing both culturable and unculturable members of the beetle gut-microbial community. Students plate beetle gut homogenates on different media, describe the colonies that are formed to estimate taxonomic diversity, extract DNA from colonies of interest, PCR amplify the16S rRNA gene for Sanger sequencing, and use the NCBI-nBLAST database to taxonomically classify sequences. Additionally, students extract total DNA from beetle gut homogenates for high-throughput paired-end sequencing and perform bioinformatic and statistical analyses of bacterial communities using a combination of open-access data processing software. Each activity allows students to engage with studies of microbiomes in a real-world context, to apply concepts and laboratory techniques to investigate either student or faculty-driven research questions, and to gain valuable experiences working with large high-throughput datasets. The CURE is designed such that it can be implemented over either 6-weeks (half semester) or 12-weeks (full semester), allowing for flexibility within the curriculum. Furthermore, student-generated data from the CURE (including bacterial colony phenotypic data, full-length 16S rRNA gene sequences from cultured isolates, and bacterial community sequences from gut homogenates) has been compiled in a continuously curated open-access database on the Bean Beetle Microbiome Project website, facilitating the generation of broader research questions across laboratory classrooms.

CUREing cancer: Development and implementation of a molecular biology-focused course-based undergraduate research experience using a cancer cell culture model.

Many students in the sciences are interested in exploring research opportunities; however, the one-on-one faculty mentorship model often lacks the ability to supervise large numbers of students. An alternative mechanism for exposing undergraduate students to the research process is participation in a Course-based Undergraduate Research Experience (CURE). CUREs promote inclusivity in research, and provide structure for both students and faculty while engaging students in scientific discovery. This study describes a model for a CURE in cancer biology, and reports student outcomes. Students utilized bioinformatics to predict targets genes of miR-100, a microRNA that is differentially expressed in a cell culture model of breast cancer metastasis. Students were required to engage with primary literature to write a grant proposal for their target gene, and then were trained to perform basic molecular biology techniques to test their individual hypotheses. Additionally, the course integrated opportunities to troubleshoot experiments and present data to the group, and culminated in a publication style scientific report discussing the results of their individual research project. Students reported significantly increased confidence in executing various molecular biology techniques and research-related skills based on pre- and post-assessment surveys. Student feedback also indicated that they gained an understanding of primary literature, experimental design, and scientific writing as a result of the course. This study supports that CUREs can be an effective pedagogy for not only engaging larger groups of students in research, but also improving their confidence and skill set in the laboratory.

Teaching virtual protein-centric CUREs and UREs using computational tools.

Readily available, free, computational approaches, adaptable for topics accessible for first to senior year classes and individual research projects, emphasizing contributions of noncovalent interactions to structure, binding and catalysis were used to teach Course-based Undergraduate Research Experiences that fulfil generally accepted main CURE components: Scientific Background, Hypothesis Development, Proposal, Experiments, Teamwork, Data Analysis of quantitative data, Conclusions, and Presentation.

A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R

Biologists with bioinformatic skills will be better prepared for the job market, but relatively few biology programs require bioinformatics courses. Inclusion in the curriculum may be hindered by several barriers, including lack of faculty expertise, student resistance to computational work, and few examples in the pedagogical literature. An 8-week wet-lab and in silico research experience for undergraduates was implemented. Students performed DNA purification and metagenomics analysis to compare the diversity and abundance of microbes in two samples. Students sampled snow from sites in northern Minnesota and purified genomic DNA from the microbes, followed by metagenomic analysis. Students used an existing metagenomic dataset to practice analysis skills, including comparing the use of Excel versus R for analysis and visualization of a large dataset. Upon receipt of the snow data, students applied their recently acquired skills to their new dataset and reported their results via a poster. Several outcomes were achieved as a result of this module. First, YouTube videos demonstrating hands-on metagenomics and R techniques were used as professional development for faculty, leading to broadened research capabilities and comfort with bioinformatics. Second, students were introduced to computational skills in a manner that was intentional, with time for both introduction and reinforcement of skills. Finally, the module was effectively included in a biology curriculum because it could function as either a stand-alone course or a module within another course such as microbiology. This module, developed with Course-based Undergraduate Research Experience guidelines in mind, introduces students and faculty to bioinformatics in biology research.

The Value of Failure: A Student-Driven Course-Based Research Experience in an Undergraduate Organic Chemistry Lab Inspired by an Unexpected Result

Research experiences are widely understood to be valuable for the intellectual and professional development of undergraduate science students. Course-based undergraduate research experiences (CUREs...

From proposal to poster: course-based undergraduate research experience in a physiology laboratory course.

The laboratory course is an excellent venue to apply content, practice inquiry, improve critical thinking, practice key clinical skills, and work with data. The use of inquiry-based course projects allows for students to propose open ended questions, form a hypothesis, design an experiment, collect data, analyze data, draw conclusion, and present their findings. This comprehensive experience is ideal for a capstone (senior level) laboratory course that is the culmination of 4 yr of study in the degree. At Michigan State University, the capstone laboratory has incorporated a formal course-based research experience in human physiology. The rationale and logistics for running such an experience are described in this paper.

Development of a Mentoring Course-Based Undergraduate Research Experience (M-CURE)

Development of a Mentoring Course-Based Undergraduate Research Experience (M-CURE)

Reflections on Course-Based Undergraduate Research in Organic and Biochemistry during COVID-19

Faculty in the Department of Chemistry and Physics at the University of New England (UNE) have recently transformed introductory and advanced chemistry curricula by embedding the high impact practice of undergraduate research. Course Based Undergraduate Research Experiences (CUREs) have provided experiential learning opportunities for over 272 students over the past three years in three different courses: University Organic Chemistry I/II (CHE 250/1 with lab), Fundamentals of Biochemistry (CHE 310/310L), and Advanced Biochemistry Laboratory (CHE 450). This communication discusses how three different faculty members in three different courses adapted workflow and curricula of chemistry CUREs laboratories to a virtual environment as dictated by the COVID-19 pandemic. Additionally, the advantages and disadvantages of curricular adaptations are discussed considering both the faculty and student experience and the importance of meeting originally defined student learning outcomes.

The Genetic Code Kit: An Open-Source Cell-Free Platform for Biochemical and Biotechnology Education.

Teaching the processes of transcription and translation is challenging due to the intangibility of these concepts and a lack of instructional, laboratory-based, active learning modules. Harnessing the genetic code in vitro with cell-free protein synthesis (CFPS) provides an open platform that allows for the direct manipulation of reaction conditions and biological machinery to enable inquiry-based learning. Here, we report our efforts to transform the research-based CFPS biotechnology into a hands-on module called the “Genetic Code Kit” for implementation into teaching laboratories. The Genetic Code Kit includes all reagents necessary for CFPS, as well as a laboratory manual, student worksheet, and augmented reality activity. This module allows students to actively explore transcription and translation while gaining exposure to an emerging research technology. In our testing of this module, undergraduate students who used the Genetic Code Kit in a teaching laboratory showed significant score increases on transcription and translation questions in a post-lab questionnaire compared with students who did not participate in the activity. Students also demonstrated an increase in self-reported confidence in laboratory methods and comfort with CFPS, indicating that this module helps prepare students for careers in laboratory research. Importantly, the Genetic Code Kit can accommodate a variety of learning objectives beyond transcription and translation and enables hypothesis-driven science. This opens the possibility of developing Course-Based Undergraduate Research Experiences (CUREs) based on the Genetic Code Kit, as well as supporting next-generation science standards in 8–12th grade science courses.

Responses to the COVID-19 Pandemic by the Biochemistry Authentic Scientific Inquiry Lab (BASIL) CURE Consortium: Reflections and a Case Study on the Switch to Remote Learning

Campus shutdowns during the SARS-CoV-2 pandemic posed unique challenges to faculty and students engaged in laboratory courses. Formerly hands-on experiments had to be quickly pivoted to emergency remote learning. While some resources existed prior to this period, many currently available online modules and/or simulations focus on a single technique. The Biochemistry Authentic Scientific Inquiry Lab (BASIL) curriculum has, for several years, provided a robust, linked, holistic inquiry experience that allows students to make connections between multiple techniques, both computational in nature as well as wet-lab-based. As a course-based undergraduate research experience (CURE), this flexible, module-based curriculum allows students to generate original hypotheses based on analysis of proteins of unknown function. We have taught this curriculum as the upper-level laboratory course on our campuses and were obliged to transition to remote instruction at various points in the course sequence. We report on the experiences of faculty and students over the transition period in this course. Additionally, we report as a case study results of one of our campus’ ongoing discipline-based education research (DBER) on the BASIL curriculum prior to and during remote delivery.

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.

Uncovering Factors Influencing Instructors' Decision Process when Considering Implementation of a Course-Based Research Experience.

Course-based undergraduate research experiences (CUREs) are an effective way to expose large numbers of students to authentic research, yet most laboratory courses still use traditional “cookbook” methods. While barriers to using CUREs have been captured postimplementation, little is known about the decision mindset before implementation or what features of CURE design may mitigate perceived barriers. Perception of an innovation (such as a CURE) influences the likelihood of its adoption, and diffusion of innovations theory posits that the decision to adopt is largely influenced by five perceived features of an innovation: relative advantage, compatibility, complexity, observability, and trialability. We conducted interviews with instructors considering using the Prevalence of Antibiotic Resistance in the Environment (PARE) project to assess their perceptions of CUREs and motivations for using PARE. Instructors viewed CUREs as having relative advantages over traditional methods; however, CUREs were also viewed as complex, with instructors citing multiple barriers. Instructors were motivated to use PARE because of its potential scientific impact and compatibility with their courses’ structures and resources. Instructors perceived PARE to have few barriers to implementation compared with other CUREs. Designing CUREs that address common instructor barriers and drivers could increase the rate of diffusion of CUREs.

Course-based Undergraduate Research Experience in a Senior Cell & Molecular Biology Laboratory Course

Course-based Undergraduate Research Experience in a Senior Cell & Molecular Biology Laboratory Course

Health Disparities in the Border Region: A Course-based Undergraduate Research Experience (CURE) with Concomitant Civic Engagement Education

Health Disparities in the Border Region: A Course-based Undergraduate Research Experience (CURE) with Concomitant Civic Engagement Education