Course-based undergraduate research experiences in molecular biosciences-patterns, trends, and faculty support

Advanced biology students' individual conceptions of scientific researchers after participating in biomedically relevant CRE

While undergraduate research has been shown to be a high-impact educational practice, it is logistically impossible for all undergraduate biology majors to have long-term faculty-mentored research experience. Therefore, biology educators and researchers must devise opportunities to engage more students in undergraduate research outside of working directly in their labs. Course-Based Research Experiences (CREs), structured as authentic research experiences, are one such opportunity. In this work, we describe the effects of a CRE with biomedical relevance on students' research skills, attitudes toward science, and perceptions of scientific research and scientific researchers. Results demonstrate that students gained experience in independent research skills including designing their own research project, being accountable for part of a project, and writing a research proposal. Students' perceptions of scientific research and researchers, assessed by the Draw-A-Researcher Task, did not show changes among the whole group, but individual analysis yielded meaningful results related to students' personal changes in how they perceived research and researchers, including their perception of themselves as researchers. This work demonstrates the substantial impact of CREs on upper-level biology undergraduate and graduate students.

Using focused ethnography to inform biomedical research infrastructure enhancement at primarily undergraduate institutions

The National Institutes of Health (NIH) supports 24 IDeA Networks of Biomedical Research Excellence (INBRE) Programs that help develop university-based biomedical research capacity in states that historically receive low levels of extramural grant support. To assess the effectiveness of the Arkansas INBRE in meeting its biomedical research capacity-building goals, we evaluated how the context (i.e., local and institutional settings) at two undergraduate institutions impacted variability in science faculty use of program resources. Data were collected by in-depth interviews with faculty and administrators (N = 9), focused observations, a review of Arkansas INBRE databases, and internet searches. Content analysis was used to code interview transcripts and field notes, and then qualitative data were integrated with data from databases and internet searches to construct two institutional case summaries. Constant comparison was used to identify similarities and differences between the institutions that helped to explain variability in how frequently faculty used Arkansas INBRE resources, including an enrollment crisis at undergraduate institutions in the United States and the presence or absence of a robust research culture at each institution. These findings were used to suggest program improvements (e.g., classroom-based research) that could further strengthen biomedical research capacity in Arkansas. As some barriers to program effectiveness are likely found in other IDeA-eligible states, improvements suggested for the Arkansas INBRE could apply to INBRE programs elsewhere.NEW & NOTEWORTHY This article describes results from an approach to program evaluation (i.e., focused ethnography) that has not been previously used to evaluate grant mechanisms. This "experience near" approach, which involved qualitative interviews and firsthand observations, lent valuable insights into how broader and institutional contexts at two primarily undergraduate institutions hindered or facilitated use of Arkansas INBRE resources. The insights gained can be used to enhance the Arkansas INBRE, which aims to strengthen the statewide biomedical infrastructure.

Using Drosophila Oogenesis in the Classroom to Increase Student Participation in Biomedical Research

Students that participate in undergraduate research benefit in multiple ways, including improved learning outcomes, increased enthusiasm for science, technology, engineering, and mathematics (STEM) fields, and increased likelihood of continuation into a STEM career. These benefits are even more pronounced for students that are traditionally under-represented in STEM, although these students often face barriers to participation in traditional apprenticeship-style research experiences. Course-based undergraduate research experiences (CUREs) are a promising and increasingly popular approach to increase undergraduate participation in research in a way that is inclusive of all students. Here, we describe how Drosophila oogenesis can be used as the basis for CUREs in a wide variety of courses. We provide an overview of our own oogenesis-based CURE, as well as suggestions for how this CURE could be adapted to accommodate a variety of schedules, course sizes, and institution types. Our goal is to simplify the process for CURE implementation in the hopes that a greater number of instructors choose to implement a CURE in their own courses.

We can do it - Empowering learning

We all need to adapt constantly in order to thrive in our ever-changing complex world. Thus, education and educators need to empower learners to develop a mindset and skills set of lifelong and lifewide learning. Papers from around the globe, reflecting the current drivers in education, were published in the FEMS Microbiology Letters virtual Thematic Issue 'Empowering learning' in October 2023. Its content is reviewed here to provide the context for further discussions within the professional community. The focus is on being inclusive, on lowering and removing barriers to learning, and fostering a sense of belonging. So learning communities can be established and connected in support of learning with and from each other for societal benefit, and this is discussed. Authentic learning approaches are highlighted with respect to the inherent opportunities for learners to take ownership for their learning, yet learn collaboratively, and develop resilience over time. Supporting learners in becoming self-regulated and realizing their full potential is truly worthwhile.

Extracellular proteins OSM-7 and OSM-8 are required for stress response gene regulation at all post-embryonic stages

Nematode cuticles are extracellular matrices (ECMs) that function as structural support and permeability barriers. Genetic disruption of specific cuticle collagen structures or secreted epidermal proteins in C. elegans activates stress response genes in epithelial cells suggesting the presence of an extracellular damage signaling mechanism. Cuticles are replaced during development via molting but investigations of extracellular signaling to stress responses have focused on adults. In our current study, we measured cuticle phenotypes and stress response gene expression in all post-embryonic stages of mutant strains for a collagen and two secreted epidermal proteins to gain insights into developmental patterns.

Development of a data science CURE in microbiology using publicly available microbiome datasets

Scientific and technological advances within the life sciences have enabled the generation of very large datasets that must be processed, stored, and managed computationally. Researchers increasingly require data science skills to work with these datasets at scale in order to convert information into actionable insights, and undergraduate educators have started to adapt pedagogies to fulfill this need. Course-based undergraduate research experiences (CUREs) have emerged as a leading model for providing large numbers of students with authentic research experiences including data science. Originally designed around wet-lab research experiences, CURE models have proliferated and diversified globally to accommodate a broad range of academic disciplines. Within microbiology, diversity metrics derived from microbiome sequence information have become standard data products in research. In some cases, researchers have deposited data in publicly accessible repositories, providing opportunities for reproducibility and comparative analysis. In 2020, with the onset of the COVID-19 pandemic and concomitant shift to remote learning, the University of British Columbia set out to develop an online data science CURE in microbiology. A team of faculty with collective domain expertise in microbiome research and CUREs developed and implemented a data science CURE in which teams of students learn to work with large publicly available datasets, develop and execute a novel scientific research project, and disseminate their findings in the online Undergraduate Journal of Experimental Microbiology and Immunology. Analysis of the resulting student-authored research articles, including comments from peer reviews conducted by subject matter experts, demonstrate high levels of learning effectiveness. Here, we describe core insights from course development and implementation based on a reverse course design model. Our approach to course design may be applicable to the development of other data science CUREs.

Curriculum Guidelines for Graduate and Undergraduate Virology Courses

Curriculum guidelines for virology are needed to best guide student learning due to the continuous and ever-increasing volume of virology information, the need to ensure that undergraduate and graduate students have a foundational understanding of key virology concepts, and the importance in being able to communicate that understanding to both other virologists and nonvirologists. Such guidelines, developed by virology educators and the American Society for Virology Education and Career Development Committee, are described herein.

Methylothon: a Versatile Course-Based High School Research Experience in Microbiology and Bioinformatics with Pink Bacteria

Methylothon is an inquiry-based high school learning module in microbial ecology, molecular biology, and bioinformatics that centers around pink-pigmented plant-associated methylotrophic bacteria. Here, we present an overview of the module's learning goals, describe course resources (available for public use at http://methylothon.com), and relate lessons learned from adapting Methylothon for remote learning during the pandemic in spring of 2021. This curriculum description is intended not only for instructors but also for microbial ecology researchers with an interest in conducting K-12 outreach. The original in-person version of the module allows students to isolate their own strains of methylotrophic bacteria from plants they sample from the environment, to identify these using PCR, sequencing, and phylogenetic analysis, and to contribute their strains to original research in a university lab. The adapted version strengthens the focus on bioinformatics and increases its flexibility and accessibility by making the lab portion optional and adopting free web-based tools. Student feedback and graded assignments from spring 2021 revealed that the lesson was especially effective at introducing the concepts of BLAST and phylogenetic trees and that students valued and felt inspired by the opportunity to conduct hands-on work and to participate in community science.

Student-Driven Course-Based Undergraduate Research Experience (CUREs) Projects in Identifying Vaginal Microorganism Species Communities to Promote Scientific Literacy Skills

Objectives

We aim to build a students' own engagement in original microbiological course-based undergraduate research experience (CUREs) model served two research and teaching scientific purposes including students' scientific literacy skills and instructors' role, which could further be applied as contribution to broader scientific knowledge and conduct novel research in their future research experience and careers.

Methods

We describe a student-driven CUREs model on the microorganism species in female vaginal using general bacterial culture techniques and high-throughput 16S rRNA gene amplicon sequencing to enable students to center experimental research method under the direction of instructors. A total of 8 undergraduate students and 5 instructors from Shanghai Jiao Tong University School of Medicine participated in the project. The CUREs were divided in four operating scopes: project planning, implementation, summarizing and feedback phases. Instructors help students to develop learning research goals.

Results

This project helped students to gain “hard skills” experiences in scientific theoretical research process and technical practices. Students reached the conclusion that Lactobacillus species dominated the primary vaginal microbiota in reproductive-age women, 16S rRNA sequencing is a method widely applied for microbiology detection. CUREs also increased students' engagement in scientific experiments and promote 3 learning goals in “soft skills”: (1) Develop students' self-study and efficacy ability, expression capability and professional research communication skills; (2) Strengthen students' motivation and ownership in science research, overcoming failure, benefitting persistence and patience, building professional science identity, competence, and confidence in collaboration, implement spirit of rigorous and carefulness; (3) Obtain authorship, independent and logical thinking capability, summarizing ability and confidence enhancement. Instructors proposed guiding research question for the students and determine evidence in achieving pedagogical goals in CUREs.

Conclusions

Our microbiological CUREs project served two scientific purposes: research and teaching, which increase students' engagement in promoting learning gains in scientific research skills, ownership, identity development, and spirit of motivation, self-efficacy, persistence, collaboration, communication, as well as opportunities to make relevant scientific discoveries. These abilities equipped them with essential foundation for the subsequent collaborative experiments and future scientific study.

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.

Transitioning Cell Culture CURE Labs from Campus to Online: Novel Strategies for a Novel Time

Course-based undergraduate research experiences (CUREs) provide a way for students to gain research experience in a classroom setting. Few examples of cell culture CUREs or online CUREs exist in the literature. The Cell Biology Education Consortium (CBEC) provides a network and resources for instructors working to incorporate cell-culture based research into the classroom. In this article, we provide examples from six instructors from the CBEC network on how they structure their cell-culture CUREs and how they transitioned the labs to online in the spring semester of 2020. We intend for these examples to provide instructors with ideas for strategies to set up cell culture CUREs, how to change that design mid-term, and for creating online CUREs in the future.

Students in a Course-Based Undergraduate Research Experience Course Discovered Dramatic Changes in the Bacterial Community Composition Between Summer and Winter Lake Samples

Course-based undergraduate research experience (CURE) courses incorporate high-impact pedagogies that have been shown to increase undergraduate retention among underrepresented minorities and women. As part of the Building Infrastructure Leading to Diversity program at the University of Detroit Mercy, a CURE metagenomics course was established in the winter of 2019. Students investigated the bacterial community composition in a eutrophic cove in Lake Saint Clair (Harrison Township, MI, United States) from water samples taken in the summer and winter. The students created 16S rRNA libraries that were sequenced using next-generation sequencing technology. They used a public web-based supercomputing resource to process their raw sequencing data and web-based tools to perform advanced statistical analysis. The students discovered that the most common operational taxonomic unit, representing 31% of the prokaryotic sequences in both summer and winter samples, corresponded to an organism that belongs to a previously unidentified phylum. This result showed the students the power of metagenomics because the approach was able to detect unclassified organisms. Principal Coordinates Analysis of Bray-Curtis dissimilarity index data showed that the winter community was distinct from the summer community [Analysis of Similarities (ANOSIM) r = 0.59829, n = 18, and p < 0.001]. Dendrograms based on hierarchically clustered Pearson correlation coefficients of phyla were divided into a winter clade and a summer clade. The conclusion is that the winter bacterial population was fundamentally different from the summer population, even though the samples were taken from the same locations in a protected cove. Because of the small class sizes, qualitative as well as statistical methods were used to evaluate the course's impact on student attitudes. Results from the Laboratory Course Assessment Survey showed that most of the respondents felt they were contributing to scientific knowledge and the course fostered student collaboration. The majority of respondents agreed or strongly agreed that the course incorporated iteration aspects of scientific investigations, such as repeating procedures to fix problems. In summary, the metagenomics CURE course was able to add to scientific knowledge and allowed students to participate in authentic research.

Integrating research into a molecular cloning course to address the evolving biotechnology landscape

The rapid development of molecular biotechnology presents a curricular challenge for educators trying to provide students with relevant coursework. A comprehensive biology education should also include opportunities for students to develop intellectual and technical skills through authentic research experiences. Integrating relevant and interesting research projects into their classes, however, can be a challenging task for instructors. To address these varied demands, we redesigned our existing molecular cloning course to incorporate an independent research project assessing calcium signaling. In the revised course, students use traditional and recombination-based cloning strategies to generate bacterial and mammalian expression vectors encoding CaMPARI, a novel fluorescent calcium indicator. Bacterially-expressed CaMPARI is used in protein quantification and purification assays. Students must also design their own research project evaluating the effect of chemotherapeutic agents on calcium signaling in a mammalian system. Revised and novel labs were designed to be modular, facilitating their integration into the course over 2 years. End-of-semester student evaluations were compared between years revealing a significant difference in students' perception of the course's difficulty between years. This change in attitude highlights potential pedagogical considerations that must be examined when introducing new material and activities into existing courses. Since calcium signaling is important for cellular process across diverse species, instructors may be able to develop research projects within their respective areas of interest. Integration of authentic research experiences into the curriculum is challenging; however, the framework described here provides a versatile structure that can be adapted to merge diverse instructor interests with evolving educational needs.

Microbiomes for All

Microbiome research projects are often interdisciplinary, involving fields such as microbiology, genetics, ecology, evolution, bioinformatics, and statistics. These research projects can be an excellent fit for undergraduate courses ranging from introductory biology labs to upper-level capstone courses. Microbiome research projects can attract the interest of students majoring in health and medical sciences, environmental sciences, and agriculture, and there are meaningful ties to real-world issues relating to human health, climate change, and environmental sustainability and resilience in pristine, fragile ecosystems to bustling urban centers. In this review, we will discuss the potential of microbiome research integrated into classes using a number of different modalities. Our experience scaling-up and implementing microbiome projects at a range of institutions across the US has provided us with insight and strategies for what works well and how to diminish common hurdles that are encountered when implementing undergraduate microbiome research projects. We will discuss how course-based microbiome research can be leveraged to help faculty make advances in their own research and professional development and the resources that are available to support faculty interested in integrating microbiome research into their courses.

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.

Be prepared - Learning for the future

Forward-looking papers from around the globe, addressing themes of current educational practice, were published in the FEMS Microbiology Letters virtual Thematic Issue 'Learning for the future' in October 2019. Its dynamic content is reviewed here to facilitate discussions within the professional community. The focus is on preparing generations of 21st century professionals as lifelong learners for yet unknown working environments and demands. Active and authentic learning is covered in various contexts from interactive lectures, via innovative tasks exploring the scientific method to conducting research over a distance. Naturally, authentic assessment features. Moreover, authentic learning is taken out of the classroom into the community as service learning for students to develop skills and see unexpected Science, Technology, Engineering and Maths career opportunities. Approaches to public engagement with science are presented including through art. Art is also brought into the classroom, as well as educational games, to foster creativity. Additionally, sharing science with large audiences on social media is discussed. Future-proofing education requires being innovative and imaginative. This comes with challenges and risks, but being prepared is worth it.

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

Over the past decade, growing evidence has shown that there are many benefits to undergraduate students engaging in scientific research, including increased persistence in pursuing STEM careers and successful outcomes in graduate study. With these benefits in mind, there has been a significant push toward providing research opportunities for students in STEM majors. To address this need, an increasing number of undergraduate courses have been developed to provide students with research experiences in a class setting, also known as course-based undergraduate research experiences, or CUREs. Despite the growing success of these courses, a number of barriers remain that deter faculty from developing and implementing CUREs. Here, we will review the perceived challenges of developing a CURE and provide practical strategies to overcome these challenges.

A laboratory competency examination in microbiology

The American Society for Microbiology's curricular guidelines for Introductory Microbiology highlighted key laboratory skills in the isolation, visualization and identification of microorganisms as core learning objectives in the discipline. Since the publication of these guidelines in 2012, there has been a paucity of diagnostic assessment tools in the literature that can be used to assess competencies in the microbiology laboratory. This project aimed to establish a laboratory competency examination for introductory microbiology, with tasks specifically aligned to laboratory skills and learning outcomes outlined in curricular guidelines for microbiology. A Laboratory Competency Examination assessing student skills in light microscopy, Gram-staining, pure culture, aseptic technique, serial dilution, dilution calculations and pipetting was developed at The University of Queensland, Australia. The Laboratory Competency Examination was field-tested in a large introductory microbiology subject (∼400 students), and student performance and learning gains data were collected from 2016 to 2017 to evaluate the validity of the assessment. The resulting laboratory assessment is presented as an endpoint diagnostic tool for assessing laboratory competency that can be readily adapted towards different educational contexts.

Analysis of Student Attitudes of a Neurobiology Themed Inquiry Based Research Experience in First Year Biology Labs

Inquiry based research experiences are thought to increase learning gains in biology, STEM retention, and confidence in students of diverse backgrounds. Furthermore, such research experiences within the first year of college may foster increased student retention and interest in biology. However, providing first year students in biology labs with inquiry-based experiences is challenging given demands of large student enrollments, restricted lab space, and instructor time. Thus, we aimed to integrate a small neurobiology themed research experience within a three-week modular, first-year biology laboratory setting. For this, students first performed a whole class lab examining the effects of ethanol on movement and associative learning. Using skills they acquired, the students devised, executed, and presented their self-designed experiments and results. Using pre-and post-course surveys, we analyzed student attitudes on their experiences, including technical skills, inquiry-based learning styles in which experimental outcomes are often unknown, and research in their first year of biology. Analyzing data collected for three years, we found that students self-reported gains in technical skills and positive attitudes toward inquiry-based learning. In contrast, we found that students did not self-report increased interest in research experiences in general.

Biochemistry laboratory reports: Filling in the introduction and discussion

Laboratory reports written in the style of a standard scientific article are commonly used to assess student learning in biochemistry laboratory courses. While most students can complete the Materials and Methods or Results sections successfully, many have difficulty with the Introduction and Discussion. They fail to place their data in a larger experimental context or to compare their results to those previously published. To address this issue in a laboratory course focusing on l-lactate dehydrogenase, a new exercise was introduced that was designed 1) to provide more background information about l-lactate dehydrogenase; 2) to give students additional experience in using PubMed and Web of Science to locate specific papers about l-lactate dehydrogenase; 3) to introduce the major bioinformatics databases at the National Center for Biological Information, ExPASy (Swiss Institute of Bioinformatics), BRENDA (Braunschweig Enzyme Database), and the Protein Data Bank; 4) to allow students to recover detailed information about l-lactate dehydrogenases; and 5) to provide practice in reading a research article that is similar to what they do in the lab. The students completed a data sheet summarizing these activities and then prepared three laboratory reports. The lab reports improved over the course of the semester and were qualitatively better than in past years. The materials developed for this laboratory course can be adapted to similar projects that use another protein as a model system. They could also be modified for use in Course-based Undergraduate Research Experiences or research projects for undergraduate or graduate students. © 2018 International Union of Biochemistry and Molecular Biology, 46(6):619-622, 2018.

Keeping education fresh-not just in microbiology

Innovative practice from around the globe, addressing a range of recent educational themes and trends, was published in the FEMS Microbiology Letters virtual Thematic Issue 'Keeping Education Fresh' in October 2017. Its thought-provoking content is reviewed here to more directly facilitate reflections and discussions in the professional community. The focus is on best practice approaches when enhancing student engagement, how to adjust those to the diversity of learners, learning situations and infrastructures, and to a broad range of subjects. The need for authentic learning and to move away from didactic teaching is emphasized. The 'students as researchers' theme is featured e.g. in context of service learning. Creative approaches are presented such as using performing arts, popular culture and gamification. The development of interdisciplinary and intercultural competences, and the exploration of socioscientific themes and philosophical issues are considered. Revisions of curricula and programmes, reflective of educational advancements and sector drivers, are discussed from undergraduate to postgraduate and professional specialist level also in light of problem-based learning, interactive distance and on-campus learning, and even the legacy of Massive Open Online Courses. Such changes always require resources and skills, and carry risks. Yet, innovation is a risk worth taking to keep education fresh.