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Course-based undergraduate research experiences (CUREs) are an effective way to integrate research into an undergraduate science curriculum and extend research experiences to a large, diverse group of early-career students. We developed a biology CURE at the University of Miami (UM) called the UM Authentic Research Laboratories (UMARL), in which groups of first-year students investigated novel questions and conducted projects of their own design related to the research themes of the faculty instructors. Herein, we describe the implementation and student outcomes of this long-running CURE. Using a national survey of student learning through research experiences in courses, we found that UMARL led to high student self-reported learning gains in research skills such as data analysis and science communication, as well as personal development skills such as self-confidence and self-efficacy. Our analysis of academic outcomes revealed that the odds of students who took UMARL engaging in individual research, graduating with a degree in science, technology, engineering, or mathematics (STEM) within 4 years, and graduating with honors were 1.5–1.7 times greater than the odds for a matched group of students from UM’s traditional biology labs. The authenticity of UMARL may have fostered students’ confidence that they can do real research, reinforcing their persistence in STEM. 

In the current report, we describe the identification of three genetically distinct groups of prophages integrated into three different chromosomal sites of human gut-associatedBifidobacterium breveandBifidobacterium longumstrains. These bifidobacterial prophages are distantly related to temperate actinobacteriophages of several hosts. Some prophages, integrated within thednaJ₂gene, are competent for induction, excision, replication, assembly and lysis, suggesting that they are fully functional and can generate infectious particles, even though permissive hosts have not yet been identified. Interestingly, several of these phages harbor a putative phase variation shufflon (the Rin system) that generates variation of the tail-associated receptor binding protein (RBP). Unlike the analogous coliphage-associated shufflon Min, or simpler Cin and Gin inversion systems, Rin is predicted to use a tyrosine recombinase to promote inversion, the first reported phage-encoded tyrosine-family DNA invertase. The identification of bifidobacterial prophages with RBP diversification systems that are competent for assembly and lysis, yet fail to propagate lytically under laboratory conditions, suggests dynamic evolution of bifidobacteria and their phages in the human gut.

 

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.