Experimental evolution of Saccharomyces cerevisiae for caffeine tolerance alters multidrug resistance and target of rapamycin signaling pathways.

Caffeine is a natural compound that inhibits the major cellular signaling regulator target of rapamycin (TOR), leading to widespread effects including growth inhibition. Saccharomyces cerevisiae yeast can adapt to tolerate high concentrations of caffeine in coffee and cacao fermentations and in experimental systems. While many factors affecting caffeine tolerance and TOR signaling have been identified, further characterization of their interactions and regulation remain to be studied. We used experimental evolution of S. cerevisiae to study the genetic contributions to caffeine tolerance in yeast, through a collaboration between high school students evolving yeast populations coupled with further research exploration in university labs. We identified multiple evolved yeast populations with mutations in PDR1 and PDR5, which contribute to multidrug resistance, and showed that gain-of-function mutations in multidrug resistance family transcription factors Pdr1, Pdr3, and Yrr1 differentially contribute to caffeine tolerance. We also identified loss-of-function mutations in TOR effectors Sit4, Sky1, and Tip41 and showed that these mutations contribute to caffeine tolerance. These findings support the importance of both the multidrug resistance family and TOR signaling in caffeine tolerance and can inform future exploration of networks affected by caffeine and other TOR inhibitors in model systems and industrial applications.

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.

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

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

Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework.

We have developed a flexible undergraduate curriculum that leverages the place-based research of environmental microbiomes to increase the number of Indigenous researchers in microbiology, data science and scientific computing. Monitoring Environmental Microbiomes (MEM) provides a curriculum and research framework designed to integrate an Indigenous approach when conducting authentic scientific research and to build interest and confidence at the undergraduate level. MEM has been successfully implemented as a short summer workshop to introduce computing practices in microbiome analysis. Based on self-assessed student knowledge of topics and skills, increased scientific confidence and interest in genomics careers were observed. We propose MEM be incorporated in a scalable course-based research experience for undergraduate institutions, including tribal colleges and universities, community colleges and other minority serving institutions. This coupled curricular and research framework explicitly considers cultural perspectives, access and equity to train a diverse future workforce that is more informed to engage in microbiome research and to translate microbiome science to benefit community and environmental health.

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

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

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.

Assessment of Course-Based Research Modules Based on Faculty Research in Introductory Biology.

Calls for early exposure of all undergraduates to research have led to the increased use and study of course-based research experiences (CREs). CREs have been shown to increase measures of persistence in the sciences, such as science identity, scientific self-efficacy, project ownership, scientific community values, and networking. However, implementing CREs can be challenging and resource-intensive. These barriers may be partly mitigated by the use of short-term CRE modules rather than semester- or year-long projects. One study has shown that a CRE module captures some of the known benefits of CREs as measured by the Persistence in the Sciences (PITS) survey. Here, we used this same survey to assess outcomes for introductory biology students who completed a semester of modular CREs based on faculty research at an R1 university. The results indicated levels of self-efficacy, science community values, and science identity similar to those previously reported for students in the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) full-semester CRE. Scores for project ownership (content) were between previously reported traditional lab and CRE scores, while project ownership (emotion) and networking were similar to those of traditional labs. Our results suggest that modular CREs can lead to significant gains in student affect measures that have been linked to persistence in the sciences in other studies. Although gains were not as great in all measures as with a semester-long CRE, implementation of modular CREs may be more feasible and offers the added benefits of exposing students to diverse research fields and lab techniques.

Infusing 21st Century Skill Development into the Undergraduate Curriculum: The Formation of the iBEARS Network.

The demonstrated gap between skills needed and skills learned within a college education places both undergraduates seeking gainful employment and the employers seeking highly skilled workers at a disadvantage. Recent and up-and-coming college graduates should possess 21st century skills (i.e., communication, collaboration, problem solving), skills that employers deem necessary for the workplace. Research shows that the development of this skillset can help narrow the gap in producing highly skilled graduates for the science, technology, engineering, and mathematics (STEM) workforce. We propose the development of 21st century skills by utilizing the project-based learning (PjBL) framework and creating the inclusive biologist exploring active research with students (iBEARS) program, allowing undergraduate students to hone their 21st century skills and prepare for transition and success within the workplace.

Course-based research experience of undergraduate medical students through project-based learning.

PURPOSE: This study aimed to design and implement an introductory-level course-based research experience (CRE) through project-based learning (PBL) for undergraduate medical students and investigate their learning experience and research skill development, with the ultimate objective of exploring whether CRE can be effectively utilized for undergraduate research experience. METHODS: This study included 40 second-year premedical students enrolled in "Scientific thinking and medical research," which was developed as an introductory-level CRE through PBL. It was a three-credit course and the students met twice a week for one semester. The students' learning experiences were examined with a 15-item survey including three open-ended questions, while their research skills were assessed through the research reports using a research skill rubric at the end of the course. RESULTS: The findings showed that the students perceived the course structure as appropriate and helpful. They also considered the group work experience to be positive and productive. Learner satisfaction items also earned positive responses in general. Regarding the research skill assessment, the mean value of the research skill scores of each group was 19.11 out of 27 and the mean value of each research skill score was 2.12 out of 3. CONCLUSION: Overall, the students were satisfied with their research experience, and their research skills were developed, suggesting that this introductory CRE through PBL can be effectively and efficiently utilized for undergraduate research experience.

The Morra Game as a Naturalistic Test Bed for Investigating Automatic and Voluntary Processes in Random Sequence Generation.

Morra is a 3,000-years-old hand game of prediction and numbers. The two players reveal their hand simultaneously, presenting a number of fingers between 1 and 5, while calling out a number between 2 and 10. Any player who successfully guesses the summation of fingers revealed by both players scores a point. While the game is extremely fast-paced, making it very difficult for players to achieve a conscious control of their game strategies, expert players regularly outperform non-experts, possibly with strategies residing out of conscious control. In this study, we used Morra as a naturalistic setting to investigate the necessity of attentive control in generation of sequence of items and the ability to proceduralize random number generation, which are both a crucial defensive strategy in Morra and a well-known empirical procedure to test the central executive capacity within the working memory model. We recorded the sequence of numbers generated by expert players in a Morra tournament in Sardinia (Italy) and by undergraduate students enrolled in a course-based research experience (CRE) course at Lawrence Technological University in the United States. Number sequences generated by non-expert and expert players both while playing Morra and in a random number generation task (RNGT) were compared in terms of randomness scores. Results indicate that expert players of Morra largely outperformed non-experts in the randomness scores only within Morra games, whereas in RNGT the two groups were very similar. Importantly, survey data acquired after the games indicate that expert players have very poor conscious recall of their number generation strategies used during the Morra game. Our results indicate that the ability of generating random sequences can be proceduralized and do not necessarily require attentive control. Results are discussed in the framework of the dual processing theory and its automatic-parallel-fast vs. controlled-sequential-slow polarities.

Role of Research Educator in sequential course-based undergraduate research experience program.

In our First-Year Research Immersion (FRI) program, students take a sequence of three CUREs (course-based undergraduate research experiences). Each Research Educator (Research Assistant Professor, aka RE) oversees the day-to-day work of about 30 first-year and 25 second-year students in a dedicated research-training lab. Instead of the typical work-load division for faculty between their teaching responsibilities (typically lecture) and research programs, REs combine these two responsibilities into one endeavour that better engages and teaches beginning students intending to major in science or engineering. Although more challenging for REs, their work in FRI expands their professional development substantially. Examples from the microbiology research track (specifically, Microbial Biofilms in Human Health) illustrate both the challenges and rewards for the REs.

Training program for Research Educators of sequential course-based undergraduate research experiences.

Science education studies have shown that a sequence of course-based research experiences has many positive effects for undergraduates. To maximize those benefits, we created a training program for the instructors (aka Research Educators). The program guides them in how to move students early in their college years through the process of science such that students then can successfully apply their learning to conduct real research projects. The key to instructors' training is creating a supportive community of practice in which everyone participates, including by taking leading roles.

Development of a Course-Based Undergraduate Research Experience to Introduce Drug-Receptor Concepts.

Course-based research experiences (CUREs) are currently of high interest due to their potential for engaging undergraduate students in authentic research and maintaining their interest in science, technology, engineering, and mathematics (STEM) majors. As part of a campus-wide initiative called STEMCats, which is a living learning program offered to freshman STEM majors at the University of Kentucky funded by a grant from Howard Hughes Medical Institute, we have developed a CURE for freshmen interested in pursuing health care careers. Our course, entitled "Drug-Drug Interactions in Breast Cancer," utilized a semester-long, in-class authentic research project and instructor-led discussions to engage students in a full spectrum of research activities, ranging from developing hypotheses and experimental design to generating original data, collaboratively interpreting results and presenting a poster at a campus-wide symposium. Student's feedback indicated a positive impact on scientific understanding and skills, enhanced teamwork and communication skills, as well as high student engagement, motivation, and STEM belonging. STEM belonging is defined as the extent to which a student may view the STEM fields as places where they belong. The results obtained from this pilot study, while preliminary, will be useful for guiding design revisions and generating appropriate objective evaluations of future pharmacological-based CUREs.