Journal of Microbiology & Biology Education

The flexibility and precision of CRISPR-Cas9 and related technologies have made these genome editing tools increasingly popular in agriculture, medicine, and basic science research over the past decade. Genome editing will continue to be relevant and utilized across diverse scientific fields in the future. Given this, students should be introduced to genome editing technologies and encouraged to consider their ethical implications early on in pre-college biology curricula. Furthermore, instruction on this topic presents an opportunity to create partnerships between researchers and educators at the K-12 levels that can strengthen student engagement in science, technology, engineering, and mathematics (STEM). To this end, we present a three-day student-centered learning program to introduce high school students to genome editing technologies through a hands-on base editing experiment in E. coli, accompanied by a relevant background lecture and facilitated ethics discussion. This unique partnership aims to educate students and provides a framework for research institutions to implement genome editing outreach programs at local high schools.

As one of the most famous fermented drinks in the world, beer is an especially relatable topic for microbiology courses. Here, we describe a short and easily adaptable module based on the antibacterial properties of hops used in brewing. By the 15th century, beer recipes included hops (the flower of the Humulus lupulus plant) as a bittering agent and antimicrobial. By the 19th century, the highly-hopped Indian Pale Ale (IPA) became popular, and a modern myth has emerged that IPAs were invented to survive long ocean voyages such as from Britain to India. With that myth in mind, we designed a hypothesis-driven microbiology lab module that tests the plausibility of this brewing myth-- namely that highly-hopped beers possess enough antibacterial activity to prevent spoilage, while lowly-hopped beers do not. The overall design of the module is to test the antimicrobial properties of hops using petri plates containing varying concentrations of hop extract. The module includes hypothesis generation and testing related to bacterial physiology and morphology (hops are not equally effective against gram-positive and gram-negative bacteria), and to mechanisms of antimicrobial resistance (as beer spoilage bacteria have repeatedly evolved hop resistance). Pre and post assessment showed that students made significant gains in the learning objectives for the module, which encourages critical thinking and hypothesis testing by linking microbial physiology and antimicrobial resistance to an important and topical real-world application.

We describe a two week Course-based Undergraduate Research Experience (CURE) to introduce students to next-generation DNA sequencing, molecular biology methods and a bioinformatic workflow. The CURE is designed to take students with little to no technical and bioinformatic experience through key steps of the protocol through scaffolded laboratory and computational practicals. Our students extract and amplify human microbiome DNA using 16S ribosomal RNA specific primers, then construct a sequencing library for Oxford Nanopore based sequencing. They taxonomically assign the sequencing reads, and determine the ecological community composition using relevant software packages. Our students were able to successfully prepare sequencing libraries and analyse the data to produce relevant figures, demonstrating they met the learning objectives of the CURE. Students identified that they had developed higher level learning as defined by Blooms taxonomy, and that their confidence in practical work significantly increased as a result of doing the CURE. We share recommendations for implementation of the CURE in undergraduate curricula, and adaptations of the methods for use in schools outreach. Our CURE successfully provides training for students in genetic analysis in an enjoyable and relatively time and cost efficient manner, preparing them for future research or careers in modern molecular biology techniques.

Understanding metabolic function requires knowledge of the dynamics, interdependence, and regulation of biochemical networks. However, current approaches are not optimal to develop the needed mechanistic understanding, and misconceptions about biological processes persist even after graduation. To address these issues, we developed a computational modeling and simulation approach that employs scaffolded learning to teach biochemistry students about the regulation of metabolism. The power of the approach lies in students abilities to alter any component or connection in a modeled system and instantly observe the effects of their changes. We find that students who use our approach perform better on biochemistry metabolism questions compared to students in a course that did not use this approach. We also investigated performance by gender and found that our modules may have the potential to increase equity in education. We noted that students are generally positive about the approach and appreciate its benefits. Our modules provide life science instructors with a dynamic and systems-driven approach to teach metabolic regulation and control that improves learning and also equips students with important technical skills.

New technologies in DNA synthesis and assembly give genetic engineers complete freedom in genetic design, where virtually any plasmid DNA sequence can be created efficiently and economically. Learning how to design, construct, and test new DNA sequences is a critical skill for researchers in molecular biology and biotechnology. Here we present a student-centered, inquiry-based module in which students learn how to control bacterial gene expression by appplying various DNA assembly techniques. The central activity in this learning module is termed the Five-Primer Challenge. Each student is allowed to order up to five 60-mer oligonucleotide primers to then modify a GFP expression plasmid with the goal of increasing GFP expression as much as possible. This module was developed and implemented at the 2016 Cold Spring Harbor Laboratory Synthetic Biology Course, and was effective at engaging students in critical thinking and in promoting student learning.

Teaching students how to conduct impactful gene expression studies within an authentic research paradigm typically relies on hands-on experience to develop skills at the bench, coupled with conceptual understanding of the experiments and their analyses within or outside of the lab setting. The unexpected shift of our gene expression laboratory course to a remote model provided the opportunity to assess how student learning of these skills and concepts would be affected in an entirely online environment. Our data suggest the reduced learning gains for skill-based techniques came with increased student learning of concepts and analysis, which may have aided stimulating student interest in gene expression studies.

In recent years, much of the emphasis for transformation of introductory STEM courses has focused on "active learning", and while this approach has been shown to produce more equitable outcomes for students, the construct of "active learning" is somewhat ill-defined, and can encompass a wide range of pedagogical techniques. Here we present an alternative approach for how to think about the transformation of STEM courses that focuses instead on what students should know and what they can do with that knowledge. This approach, known as three-dimensional learning (3DL), emerged from the National Academys "A Framework for K-12 Science Education", which describes a vision for science education that centers the role of constructing productive causal accounts for phenomena. Over the past 10 years, we have collected data from introductory biology, chemistry, and physics courses to assess the impact of such a transformation on higher education courses. Here we report on an analysis of video data of class sessions that allows us to characterize these sessions as active, 3D, neither, or both 3D and active. We find that 3D classes are likely to also involve student engagement (i.e. be active), but the reverse is not necessarily true. That is, focusing on transformations involving 3DL also tends to increase student engagement, whereas focusing solely on student engagement might result in courses where students are engaged in activities that do not involve meaningful engagement with core ideas of the discipline.

Modern molecular biology tools and technologies such as CRISPR have sped up scientific discovery. From an educational perspective, these advancements are both exciting and overwhelming. Educators shaping these future scientists face the ongoing challenge of staying compliant with the latest developments in molecular biology while finding effective ways to teach these discoveries. As the use of CRISPR gene editing technology continues to expand globally, there is an increasing need for a workforce that is both knowledgeable about its theoretical foundations and trained in its practical use. While advanced, technology-driven STEM courses have the potential to improve student retention, they are often lecture-heavy and lack intentional engagement strategies that support deeper learning. Moreover, agriculture is the second most impacted sector by this technology, yet there is a significant lack of teaching materials focused on CRISPR in plant biology. To address these gaps, we developed a framework for teaching gene editing that incorporates multiple engagement strategies beyond traditional lecture-based instruction. This framework was implemented over two semesters in an Introduction to Gene Editing course at Tennessee State University, offered to both undergraduate and graduate students enrolled in a degree in Agricultural Sciences. This manuscript outlines the various strategies used in the course including active learning, multimodal instructional approaches and experiential learning strategies that can be adopted in other classrooms to effectively teach gene editing. Survey-based results from the course indicate a measurable increase in student comfort with designing and executing CRISPR-Cas based experiments. Societal Impact StatementPlant biology lacks accessible teaching materials for CRISPR, a powerful gene-editing technology widely used to improve agriculture. We developed an engaging framework to teach CRISPR concepts to advanced undergraduates and graduate students in plant sciences, which can be readily adopted by other instructors. The approach increased self-reported confidence in students and comfort in explaining CRISPR. Since instructors often have limited time to design interactive lessons, this framework offers a ready-to-use, effective strategy that makes CRISPR more widely available in classrooms, ultimately strengthening CRISPR literacy in the future agricultural workforce.

The Fly-CURE is a genetics-focused multi-institutional Course-Based Undergraduate Research Experience (CURE) that provides undergraduate students with hands-on research experiences within a course. Through the Fly-CURE, undergraduate students at diverse types of higher education institutions across the United States map and characterize novel mutants isolated from a genetic screen in Drosophila melanogaster. To evaluate the impact of the Fly-CURE experience on students, we developed and validated assessment tools to identify students perceived research self-efficacy, sense of belonging in science, and intent to pursue additional research opportunities. Our data show gains in these metrics after completion of the Fly-CURE across all student subgroups analyzed, including comparisons of gender, academic status, racial and ethnic groups, and parents educational background. Importantly, our data also show differential gains in the areas of self-efficacy and interest in seeking additional research opportunities between Fly-CURE students with and without prior research experience, illustrating the positive impact of research exposure (dosage) on student outcomes. Altogether, our data indicate that the Fly-CURE experience has a significant impact on students efficacy with research methods, sense of belonging to the scientific community, and interest in pursuing additional research experiences.

The concept of biofilms and biofilm-based research is largely absent or minimally described in high school and undergraduate life science curriculum. While it is well-established that microbes, such as bacteria and fungi most often exist in multicellular biofilm communities, descriptions in standard biology textbooks continue to focus on the single-celled form of microbial life. We have developed an analogy-based instructional tool to introduce and explain biofilms to high school and undergraduate students. The module employs an analogy with beehives, given that biofilms and beehives are both superorganism states, to explain key biofilm features such as development and structure, chemical communication, division of labor and emergent properties. We delivered this analogy based learning tool to a cohort of 49 high school and undergraduate students, and based on participant feedback and learnings, present a formal evaluation of the instructional tool. Further, we outline prerequisites and learning approaches that can enable the delivery of this module in classroom and virtual learning settings, including suggestions for pre-lesson reading, student-centred interactive activities, and specific learning objectives. Taken together, this instructional analogy holds potential to serve as an educational tool to introduce biofilms in high school and undergraduate curricula in a relatable and comprehensible manner.

The restructuring of an upper division biochemistry lab capstone course intended for biochemistry students with a range of laboratory experience was explored. A goal of the course was to give students practice with necessary skills in biochemical and biological techniques, especially for an entry level general position in biotechnology. The immediate impact of the online capstone course mandated by the COVID-19 pandemic limited students on learning essential hands-on research skills but evolved during the transition back to in-person instruction to include more elements of in-person practice. This article highlights the evolution of the capstone biochemistry lab to an in-person CURE capstone lab, with lessons learned and resources successfully used during the COVID-19 remote course. These include changes in the way information was disseminated, access to online resources, and modifications in student assessments. This article documents how course evolution resulted in a shift in pedagogical strategies leading to building a community of biochemistry learners that could be used to help college faculty in developing a CURE capstone lab.

The multi-disciplinary nature of science, technology, engineering and math (STEM) careers often renders difficulty for high school students navigating from classroom knowledge to post-secondary pursuits. Discrepancies between the knowledge-based high school learning approach and the experiential approach of undergraduate studies leaves some students disillusioned by STEM. We present Discovery, a semester-long inquiry-focused learning model delivered by STEM graduate students in collaboration with high school educators, in the context of biomedical engineering. Entire classes of high school STEM students representing diverse cultural and socioeconomic backgrounds engaged in iterative, problem-based learning designed to emphasize critical thinking concomitantly within the secondary school and university environments. Assessment of grades and survey data suggested positive impact of this learning model on students STEM pursuits, notably in under-performing cohorts, as well as repeating cohorts that engage in the program on more than one occasion. Discovery presents a scalable platform blurring the divide between secondary and post-secondary learning, providing valuable learning opportunities and capturing cohorts of students that might otherwise be under-engaged in STEM.

Intensive postgraduate courses provide an opportunity for junior and senior level scientists to learn concepts and techniques that will advance their training and research programs. It is commonly assumed that short intensive courses have positive impacts within fields of research; however, these assumptions are rarely tested. Here we describe the framework of a long running postgraduate summer course at Cold Spring Harbor and attempt to quantify the impact made over its history. For over three decades, the Drosophila Neurobiology: Genes, Circuits & Behavior Summer Course at Cold Spring Harbor Laboratories (CSHL) has provided participants with intense instruction on a wide variety of topics and techniques in integrative neuroscience using Drosophila as a model organism. Students are introduced to the latest approaches for studying nervous system development, activity and connectivity, as well as complex behaviors and diseases. The course has a long history of successful alumni, many of whom describe participation in the course as foundational to their training. Student surveys of recent participants indicate a high level of satisfaction, improved career outcomes, and direct impact on publications. Analysis of student success reveals that over 64% of participants obtain independent faculty positions. Further, we describe ongoing efforts to enhance diversity and encourage access to scientific research at undergraduate-focused institutions. Together, our findings suggest that laboratory-intensive postgraduate courses provide a highly effective mechanism for scientific training that has lasting positive impacts on trainees.

Teamwork is recognized as critical to solving complex societal challenges related to energy, health, and sustainability. With graduate education, students often gain teamwork experience through a problem-focused approach where they are brought into existing collaborations to pursue research that is focused on studying questions that have already been identified. Here, we describe an interdisciplinary educational program where graduate students were tasked with leading team formation, problem identification, and research formulation. This "team-first" training approach used a two-year curriculum to bring together students enrolled in diverse engineering and science graduate programs and provided students with a pedagogical understanding of interdisciplinarity, nurtured the development of student communication skills across disciplines, fostered student-led team formation and idea development, and empowered students to forge new connections between research groups. Assessment of three cohorts immediately following curriculum completion (n = 36) revealed significant gains in confidence in teamwork (p < 0.001) when compared to a control group of academic peers (n = 74). These gains varied across demographic groups, with women in science, technology, engineering, and mathematics presenting the strongest gains. This finding illustrates the importance of exploring how interdisciplinary team curricula in graduate school could support overcoming the gender gap in confidence. SignificancePedagogical models for graduate education often neglect the importance of teamwork training. Here, we describe an interdisciplinary training program that was developed to bring together doctoral students from diverse science, technology, engineering, and mathematics disciplines for a two-year curriculum that focused on teamwork training through student-led team formation, problem identification, and research formulation. Following program participation, we measured participant confidence in teamwork relative to a peer group. Our findings reveal gains with confidence in teamwork, with women presenting the strongest increases without negative effects on other groups. This pedagogical approach represents a strategy to close gender gaps in professional role confidence while complementing the benefits of traditional disciplinary training approaches.

Post-baccalaureate (post-bac) programs can be instrumental in strengthening science training and expanding STEM career opportunities for junior trainees. Many of these sponsored programs are designed to increase research exposure for underrepresented minorities, including African American, Hispanic, Native American, and first-generation college students, among others. Recruiting trainees to post-bac programs can be challenging for reasons including a lack of awareness about available programs. To address this gap, an Open House event was created with the goal of raising awareness and generating interest among potential students for future post-bac programs. Students were recruited from partnering Minority Serving Institutions (MSIs) to attend a two-day event at a Primarily Undergraduate Institution (PUI) and a Research-Intensive (R1) institution. During the visit, students toured both campuses, learned about various post-bac programs and research opportunities, and interacted with faculty, current graduate students, and a former post-bac scholar. Transportation, lodging, and meals were provided. Participants completed voluntary pre- and post-surveys. Results indicated that attendees, the majority of whom were underrepresented minorities in STEM, left with a stronger understanding of post-bac programs and how these experiences could support their future careers in STEM and that students attendance at the event made it more likely they would apply to available post-bac programs. Mentor and MSI faculty survey responses highlighted their strong support for participating in future recruitment events. These findings demonstrate that in-person Open House events, built on collaborative partnerships across institutions, are an effective strategy for increasing awareness and encouraging participation in post-bac training programs-- particularly among underrepresented student populations.

AO_SCPLOWBSTRACTC_SCPLOWIncreasing diversity in the biomedical research workforce is a critical national issue. Particularly concerning is the lack of representation at more advanced career stages/in leadership positions. While there are numerous institutional initiatives promoting professional research skills (i.e. grant writing, presenting, networking) for underrepresented (UR) PhD trainees, there are comparatively fewer opportunities for leadership development. We present a blueprint for Leadership in PhD (LeaP), a cohort-based program aiming to equip UR biomedical research trainees with skills to succeed as academic, industry, and community leaders. In contrast to intensive short-term programs or workshops, LeaP is a longitudinal 4-year experience with an emphasis on self-directed and experiential learning. First year trainees receive foundational didactic instruction on core leadership concepts coupled with facilitated peer discussions and one-on-one coaching support. We outline a program evaluation framework that assesses student learning, satisfaction, and program efficacy. Evaluation data from the inaugural year is presented and discussed.

The biomedical sciences have a problem retaining white women and underrepresented minorities in academia. Despite increases in the representation of these groups in faculty candidate pools, they are still underrepresented at the faculty level, particularly at the Full Professor level. The lack of diverse individuals at the Full Professor level contributes to the attrition of women and under-represented minorities, as it confirms unconscious biases. The presence of unconscious biases contribute to feelings of not belonging by trainees and are amplified by visual representation of who is presented as the \"top scientist in their field\". Top scientists are not only defined by the attainment of Full Professorships, but also through invited seminar series. Invitations for faculty to present their research at other university departments is highly valued offer that provides an opportunity for collaborations and networking. However, if invited speakers do not represent the demographics of current trainees, these visual representations of successful scientists may contribute to decreased attitudes of self-identification as a scientist, ultimately resulting in trainees leaving the field or the academy. In this study, we compare invited-speaker demographics to the current trainee demographics in one microbiology and immunology department and find that trainees are not proportionally represented by speakers invited to the department. Our investigation prompted changes in policy for how invited speakers are selected in the future to invite a more diverse group of scientists. To facilitate this process, we developed a set of tips and a web-based resource that allows scientists, committees, and moderators to identify members of under-served groups. These resources can be easily adapted by other fields or sub-fields to promote inclusion and diversity at seminar series, conferences, and colloquia.

A common problem in the biotech sector of developing countries is that a large portion of students attain a poor conceptual understanding of the basic theory and/or lack proficiency in basic laboratory skills even as they complete higher studies such as a masters degree. A small scale solution was developed in the form of a unique post-graduate diploma program that imparted reliable skills in students with good theoretical knowledge. The course of 6 to 8 months duration, with an optional 6 months internship, was successfully conducted for 8 batches. Most students of this course inculcated the right laboratory practices. This was evident by safe operations, and precise as well as accurate results of quantitative experiments conducted by them. They learned to work independently as well as in teams. They could create and follow standard operating procedures, and contribute to general laboratory maintenance. Every student also designed, prepared and conducted routine molecular biology experiments. The following aspects are suggested for successfully dealing with the patchy and varied capacities of life science students during higher (post bachelors) studies: a) careful selection of students, b) training with prioritized objectives, c) attention to basic lab-practices, d) opportunities to self-learn, e) structured group discussions, f) teacher(s) with genuine interest and passion, g) reasonable infrastructure, and h) maintaining a good student-instructor ratio. The course objectives, structure, teaching methods, and experiences are presented here along with some of the relevant data, including statistics about improvement in the precision and accuracy in experimental results by students. Limitations in this course and a general critical perspective of the routine higher education have also been discussed briefly.

We introduce LeDNA, a versatile educational toolkit designed for teaching fundamental genetics and CRISPR-Cas gene editing principles in diverse settings, regardless of existing infrastructure. Fabricated using laser-cutting techniques, LeDNA is an open-source resource suitable for students across educational levels, from high school to graduate studies. Given the transformative potential of CRISPR technology in various fields, including medicine and agriculture, a widespread understanding of its principles is essential for informed public discourse and acceptance. By providing a readily accessible and affordable tool, LeDNA aims to democratize genetics and CRISPR education globally, fostering a more informed and engaged community.

The development of mathematical and quantitative skills is increasingly critical for biology students. Literacy in coding, statistics, and mathematical modeling enables students to engage in systems-thinking and the analysis of large data sets. Here we present a flexible tool illustrating concepts in mathematical modeling, coding, and biology for integration into both traditional cookbook and inquiry-driven labs for freshmen biology students. We developed simple and complex mathematical models of potato catechol oxidase, a popular system to teach enzyme kinetics in undergraduate biology labs. We integrated both models into a freely-available web app for simulation and parameter estimation. The models are usable even if experimental details are unknown or poorly controlled, so that even novice students can work through the problem. We illustrate this by estimating the kinetic parameters of catechol oxidase in the complex model using data obtained from two sections of a course-based undergraduate research experience (CURE) freshman biology lab. Worksheets with questions motivating model building and simulation comprehension are provided. The effect of these exercises on students opinions of math, biology, and coding are evaluated using pre- and post-test surveys and student feedback. Our results show that these tools illustrate enzyme kinetics mathematically, students are not intimidated by the degree of math or coding involved, and in some cases are interested to do more, despite being unaware of the focus of the lab when signing up.