David J. Asai

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

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. DOI: http://dx.doi.org/10.7554/eLife.06416.001

Partnered research experiences for junior faculty at minority-serving institutions enhance professional success.

This paper describes achievements of faculty in federal funding, publication, and other areas following their participation in the Visiting Professorship (VP) Program. Achievements of participants were compared to those of matched peers and showed marked improvement following their VP experiences.

Analysis of Properties of Cilia Using Tetrahymena thermophila

Cilia and eukaryotic flagella are important structures required for the motility of cells, the movement of medium across the surfaces of cells, and the connections between the receptor and synthetic portions of sensory cells. The axoneme forms the cytoskeleton of the cilium comprising several hundreds of proteins that assemble into the 9 + 2 arrangement of outer doublet and central pair microtubules, the inner and outer rows of dynein arms, and many other structures. Tetrahymena thermophila is an excellent model organism for the study of cilia and ciliogenesis. The cell is covered by about 1,000 cilia which are essential for survival. Additionally, the Tetrahymena genome is available and targeted genetic manipulations are straightforward. In this chapter, we describe five protocols that examine properties of cilia: (a) measuring mRNA levels to see the effect of deciliation on gene expression; (b) swimming velocity and linearity; (c) ciliary length and density; (d) phagocytosis that occurs through the ciliated oral apparatus; and (e) depolarization-induced ciliary reversal.

Measuring Student Development

For the past two decades, funding organizations such as mine have supported initiatives at U.S. colleges and universities with the goal of transforming undergraduate science education. Now it is time to ask the tough questions: How effective have these efforts been? How can educators and funders build on the lessons learned? Undergraduate education is an absolutely critical enterprise. Regardless of the future profession that a student chooses, this is the time when undergraduates acquire the fundamental skills for making creative contributions to society, including the process of scientific thinking that will empower them to be more effective citizens.

Not just Salk

In her Science Insider News Story “Salk Institute hit with discrimination lawsuit by third female scientist” (20 July, ) M. Wadman reports that three of the four senior women scientists at the Salk Institute have filed a lawsuit alleging gender discrimination. The

From HHMI: Doubling Down on Diversity

In spite of modest gains in the past 50 years, the United States has not been able to substantially improve on the pervasive underrepresentation of minorities in postsecondary STEM pathways. We suggest a way to guide a national effort to double the persistence of underrepresented minorities in STEM in the next decade.

UNIT 9.2 Immunofluorescence Microscopy

The visualization of fluorescently tagged molecules is a powerful strategy that can contribute to the understanding of the complex dynamics of the cell. A particularly robust and broadly applicable method is immunofluorescence microscopy, in which a specific fluorescently labeled antibody binds the molecule of interest and then the location of the antibody is determined by fluorescence microscopy. The effective application of this technique includes several considerations, including the nature of the antigen, specificity of the antibody, permeabilization and fixation of the specimen, and fluorescence imaging of the cell. Although each protocol will require fine‐tuning depending on the cell type, the antibody, and the antigen, there are steps common to nearly all applications. This unit provides protocols for visualization of the cytoskeleton in two very different kinds of cells: flat, adherent fibroblasts and thick, free‐swimming Tetrahymena cells.