A low-cost cure for CUREs: An undergraduate microbiology course engaging students in authentic research using publicly available datasets.

Undergraduate research experiences are key to preparing STEM students for a range of careers and graduate programs, and to impacting retention in STEM. Providing undergraduate research experiences can be challenging for institutions due to the high cost associated with equipment and reagents, lab space, and research mentors. In this study, we present an upper-level microbiology seminar course that does not require these resources, as each student chooses and performs their own research project using data obtained from publicly available datasets. The faculty member provides hands-on instruction and regular feedback to mentor the cohort of students through all stages of their research projects, from honing a research question, to choosing a dataset, to data analysis and visualization. Students build science communication skills through each writing a scientific paper, and creating and presenting a scientific poster. These papers and presentations, along with results from student pre- and post-surveys, demonstrate that students built research and communication skills, while also building their confidence and interest in science careers. To access this research experience, students only need to register for this course; no application or selection is required, and no prior research experience is expected. The use of publicly available data makes this course a low-cost way to integrate authentic research projects into the college curriculum, and can be adapted to courses in any discipline. Such "low-cost CUREs" (course-based undergraduate research experiences) can be used to build capacity for undergraduate research experiences that are so crucial to preparing students for opportunities in and beyond college.

Tetraploidy accelerates adaptation under drug selection in a fungal pathogen.

Baseline ploidy significantly impacts evolutionary trajectories and, specifically, tetraploidy is associated with higher rates of adaptation relative to haploidy and diploidy. While the majority of experimental evolution studies investigating ploidy use the budding yeast Saccharomyces cerivisiae, the fungal pathogen Candida albicans is a powerful system to investigate ploidy dynamics, particularly in the context of acquiring antifungal drug resistance. C. albicans laboratory and clinical strains are predominantly diploid, but have been isolated as haploid and polyploid. Here, we evolved diploid and tetraploid C. albicans for ~60 days in the antifungal drug caspofungin. Tetraploid-evolved lines adapted faster than diploid-evolved lines and reached higher levels of caspofungin resistance. While diploid-evolved lines generally maintained their initial genome size, tetraploid-evolved lines rapidly underwent genome-size reductions and did so prior to caspofungin adaptation. While clinical resistance was largely due to mutations in FKS1, these mutations were caused by substitutions in diploid, and indels in tetraploid isolates. Furthermore, fitness costs in the absence of drug selection were significantly less in tetraploid-evolved lines compared to the diploid-evolved lines. Taken together, this work supports a model of adaptation in which the tetraploid state is transient but its ability to rapidly transition ploidy states improves adaptive outcomes and may drive drug resistance in fungal pathogens.

The Magnitude of Candida albicans Stress-Induced Genome Instability Results from an Interaction Between Ploidy and Antifungal Drugs.

Organismal ploidy and environmental stress impact the rates and types of mutational events. The opportunistic fungal pathogen Candida albicans, serves as a clinically relevant model for studying the interaction between eukaryotic ploidy and drug-induced mutagenesis. In this study, we compared the rates and types of genome perturbations in diploid and tetraploid C. albicans following exposure to two different classes of antifungal drugs; azoles and echinocandins. We measured mutations at three different scales: point mutation, loss-of-heterozygosity (LOH), and total DNA content for cells exposed to fluconazole and caspofungin. We found that caspofungin induced higher mutation rates than fluconazole, although this is likely an indirect consequence of stress-associated cell wall perturbations, rather than an inherent genotoxicity. Surprisingly, we found that antifungal drugs disproportionately elevated genome and ploidy instability in tetraploid C. albicans compared to diploids. Taken together, our results suggest that the magnitude of stress-induced mutagenesis results from an interaction between ploidy and antifungal drugs. These findings have both clinical and evolutionary implications for how fungal pathogens generate mutations in response to antifungal drug stress and how these mutations may facilitate the emergence of drug resistance.