Synthesizing Research Narratives to Reveal the Big Picture: a CREATE(S) Intervention Modified for Journal Club Improves Undergraduate Science Literacy.

Communicating science effectively is an essential part of the development of science literacy. Research has shown that introducing primary scientific literature through journal clubs can improve student learning outcomes, including increased scientific knowledge. However, without scaffolding, students can miss more complex aspects of science literacy, including how to analyze and present scientific data. In this study, we apply a modified CREATE(S) process (Concept map the introduction, Read methods and results, Elucidate hypotheses, Analyze data, Think of the next Experiment, and Synthesis map) to improve students' science literacy skills, specifically their understanding of the process of science and their ability to use narrative synthesis to communicate science. We tested this hypothesis using a retrospective quasi-experimental study design in upper-division undergraduate courses. We compared learning outcomes for CREATES intervention students to those for students who took the same courses before CREATES was introduced. Rubric-guided, direct evidence assessments were used to measure student gains in learning outcomes. Analyses revealed that CREATES intervention students versus the comparison group demonstrated improved ability to interpret and communicate primary literature, especially in the methods, hypotheses, and narrative synthesis learning outcome categories. Through a mixed-methods analysis of a reflection assignment completed by the CREATES intervention group, students reported the synthesis map as the most frequently used step in the process and highly valuable to their learning. Taken together, the study demonstrates how this modified CREATES process can foster scientific literacy development and how it could be applied in science, technology, engineering, and math journal clubs.

Novel Cluster AZ Arthrobacter phages Powerpuff, Lego, and YesChef exhibit close functional relationships with Microbacterium phages.

Bacteriophages exhibit a vast spectrum of relatedness and there is increasing evidence of close genomic relationships independent of host genus. The variability in phage similarity at the nucleotide, amino acid, and gene content levels confounds attempts at quantifying phage relatedness, especially as more novel phages are isolated. This study describes three highly similar novel Arthrobacter globiformis phages-Powerpuff, Lego, and YesChef-which were assigned to Cluster AZ using a nucleotide-based clustering parameter. Phages in Cluster AZ, Microbacterium Cluster EH, and the former Microbacterium singleton Zeta1847 exhibited low nucleotide similarity. However, their gene content similarity was in excess of the recently adopted Microbacterium clustering parameter, which ultimately resulted in the reassignment of Zeta1847 to Cluster EH. This finding further highlights the importance of using multiple metrics to capture phage relatedness. Additionally, Clusters AZ and EH phages encode a shared integrase indicative of a lysogenic life cycle. In the first experimental verification of a Cluster AZ phage's life cycle, we show that phage Powerpuff is a true temperate phage. It forms stable lysogens that exhibit immunity to superinfection by related phages, despite lacking identifiable repressors typically required for lysogenic maintenance and superinfection immunity. The ability of phage Powerpuff to undergo and maintain lysogeny suggests that other closely related phages may be temperate as well. Our findings provide additional evidence of significant shared phage genomic content spanning multiple actinobacterial host genera and demonstrate the continued need for verification and characterization of life cycles in newly isolated phages.

BlueFeather, the singleton that wasn't: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE.

Bacteriophages (phages) exhibit high genetic diversity, and the mosaic nature of the shared genetic pool makes quantifying phage relatedness a shifting target. Early parameters for clustering of related Mycobacteria and Arthrobacter phage genomes relied on nucleotide identity thresholds but, more recently, clustering of Gordonia and Microbacterium phages has been performed according to shared gene content. Singleton phages lack the nucleotide identity and/or shared gene content required for clustering newly sequenced genomes with known phages. Whole genome metrics of novel Arthrobacter phage BlueFeather, originally designated a putative singleton, showed low nucleotide identity but high amino acid and gene content similarity with Arthrobacter phages originally assigned to Clusters FE and FI. Gene content similarity revealed that BlueFeather shared genes with these phages in excess of the parameter for clustering Gordonia and Microbacterium phages. Single gene analyses revealed evidence of horizontal gene transfer between BlueFeather and phages in unique clusters that infect a variety of bacterial hosts. Our findings highlight the advantage of using shared gene content to study seemingly genetically isolated phages and have resulted in the reclustering of BlueFeather, a putative singleton, as well as former Cluster FI phages, into a newly expanded Cluster FE.

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom.

Improvements in high-throughput sequencing makes targeted amplicon analysis an ideal method for the study of human and environmental microbiomes by undergraduates. Multiple bioinformatics programs are available to process and interpret raw microbial diversity datasets, and the choice of programs to use in curricula is largely determined by student learning goals. Many of the most commonly used microbiome bioinformatics platforms offer end-to-end data processing and data analysis using a command line interface (CLI), but the downside for novice microbiome researchers is the steep learning curve often required. Alternatively, some sequencing providers include processing of raw data and taxonomy assignments as part of their pipelines. This, when coupled with available web-based or graphical user interface (GUI) analysis and visualization tools, eliminates the need for students or instructors to have extensive CLI experience. However, lack of universal data formats can make integration of these tools challenging. For example, tools for upstream and downstream analyses frequently use multiple different data formats which then require writing custom scripts or hours of manual work to make the files compatible. Here, we describe a microbial ecology bioinformatics curriculum that focuses on data analysis, visualization, and statistical reasoning by taking advantage of existing web-based and GUI tools. We created the Program for Unifying Microbiome Analysis Applications (PUMAA), which solves the problem of inconsistent files by formatting the output files from several raw data processing programs to seamlessly transition to a suite of GUI programs for analysis and visualization of microbiome taxonomic and inferred functional profiles. Additionally, we created a series of tutorials to accompany each of the microbiome analysis curricular modules. From pre- and post-course surveys, students in this curriculum self-reported conceptual and confidence gains in bioinformatics and data analysis skills. Students also demonstrated gains in biologically relevant statistical reasoning based on rubric-guided evaluations of open-ended survey questions and the Statistical Reasoning in Biology Concept Inventory. The PUMAA program and associated analysis tutorials enable students and researchers with no computational experience to effectively analyze real microbiome datasets to investigate real-world research questions.

Genomic diversity of bacteriophages infecting Microbacterium spp.

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations.

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results.

Comparing the Impact of Course-Based and Apprentice-Based Research Experiences in a Life Science Laboratory Curriculum.

This four-year study describes the assessment of a bifurcated laboratory curriculum designed to provide upper-division undergraduate majors in two life science departments meaningful exposure to authentic research. The timing is critical as it provides a pathway for both directly admitted and transfer students to enter research. To fulfill their degree requirements, all majors complete one of two paths in the laboratory program. One path immerses students in scientific discovery experienced through team research projects (course-based undergraduate research experiences, or CUREs) and the other path through a mentored, independent research project (apprentice-based research experiences, or AREs). The bifurcated laboratory curriculum was structured using backwards design to help all students, irrespective of path, achieve specific learning outcomes. Over 1,000 undergraduates enrolled in the curriculum. Self-report survey results indicate that there were no significant differences in affective gains by path. Students conveyed which aspects of the curriculum were critical to their learning and development of research-oriented skills. Students' interests in biology increased upon completion of the curriculum, inspiring a subset of CURE participants to subsequently pursue further research. A rubric-guided performance evaluation, employed to directly measure learning, revealed differences in learning gains for CURE versus ARE participants, with evidence suggesting a CURE can reduce the achievement gap between high-performing students and their peers.

Strategies for using peer-assisted learning effectively in an undergraduate bioinformatics course.

This study used a mixed methods approach to evaluate hybrid peer-assisted learning approaches incorporated into a bioinformatics tutorial for a genome annotation research project. Quantitative and qualitative data were collected from undergraduates who enrolled in a research-based laboratory course during two different academic terms at UCLA. Findings indicate that a critical feature of the peer-assisted learning approach is to have near-peer leaders with genome annotation experience, allowing them to communicate technical and conceptual aspects of the process in the context of a research project (a.k.a., the "big picture"). These characteristics are important for creating connections between the wet lab experiments and the computer lab activities, engendering excitement about the research project and fostering engagement in bioinformatics as a discipline. Likewise, it is essential to couple tutorial training in genome annotation with appropriate instructional materials, providing detailed, step-by-step instructions for database navigation. Finally, the assessment results support this hybrid peer-assisted learning approach as a model for undergraduates to successfully learn bioinformatics in a course setting.