From HHMI: Doubling Down on Diversity.

In spite of modest gains in the past four decades, the United States has not been able to substantially improve on the pervasive underrepresentation of minorities in postsecondary science, technology, engineering, and mathematics (STEM) pathways. We suggest a way to guide a national effort to double the persistence of underrepresented minorities in STEM in the next decade.

The Faculty Self-Reported Assessment Survey (FRAS): differentiating faculty knowledge and experience in assessment.

Science, technology, engineering, and mathematics education reform efforts have called for widespread adoption of evidence-based teaching in which faculty members attend to student outcomes through assessment practice. Awareness about the importance of assessment has illuminated the need to understand what faculty members know and how they engage with assessment knowledge and practice. The Faculty Self-Reported Assessment Survey (FRAS) is a new instrument for evaluating science faculty assessment knowledge and experience. Instrument validation was composed of two distinct studies: an empirical evaluation of the psychometric properties of the FRAS and a comparative known-groups validation to explore the ability of the FRAS to differentiate levels of faculty assessment experience. The FRAS was found to be highly reliable (α = 0.96). The dimensionality of the instrument enabled distinction of assessment knowledge into categories of program design, instrumentation, and validation. In the known-groups validation, the FRAS distinguished between faculty groups with differing levels of assessment experience. Faculty members with formal assessment experience self-reported higher levels of familiarity with assessment terms, higher frequencies of assessment activity, increased confidence in conducting assessment, and more positive attitudes toward assessment than faculty members who were novices in assessment. These results suggest that the FRAS can reliably and validly differentiate levels of expertise in faculty knowledge of assessment.

A new system for comparative functional genomics of Saccharomyces yeasts.

Whole-genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a genome-wide functional characterization of a sequenced but experimentally understudied budding yeast, Saccharomyces bayanus var. uvarum (henceforth referred to as S. bayanus), allowing us to map changes over the 20 million years that separate this organism from S. cerevisiae. We first created a suite of genetic tools to facilitate work in S. bayanus. Next, we measured the gene-expression response of S. bayanus to a diverse set of perturbations optimized using a computational approach to cover a diverse array of functionally relevant biological responses. The resulting data set reveals that gene-expression patterns are largely conserved, but significant changes may exist in regulatory networks such as carbohydrate utilization and meiosis. In addition to regulatory changes, our approach identified gene functions that have diverged. The functions of genes in core pathways are highly conserved, but we observed many changes in which genes are involved in osmotic stress, peroxisome biogenesis, and autophagy. A surprising number of genes specific to S. bayanus respond to oxidative stress, suggesting the organism may have evolved under different selection pressures than S. cerevisiae. This work expands the scope of genome-scale evolutionary studies from sequence-based analysis to rapid experimental characterization and could be adopted for functional mapping in any lineage of interest. Furthermore, our detailed characterization of S. bayanus provides a valuable resource for comparative functional genomics studies in yeast.

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.

A rapid PCR-RFLP method for monitoring genetic variation among commercial mushroom species*.

We report the development of a simplified procedure for restriction fragment length polymorphism (RFLP) analysis of mushrooms. We have adapted standard molecular techniques to be amenable to an undergraduate laboratory setting in order to allow students to explore basic questions about fungal diversity and relatedness among mushroom species. The streamlined protocols allowed students to practice important molecular techniques within the context of self-designed investigative projects. This laboratory experience provided opportunities for students to practice strategies for examining molecular diversity among species.