While course-based research in genomics can generate both knowledge gains and a greater appreciation for how science is done, a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. Nonetheless, this is a very cost-effective way to reach larger numbers of students.

There have been numerous calls to engage students in science as science is done. A survey of 90-plus faculty members explores barriers and incentives when developing a research-based genomics course. The results indicate that a central core supporting a national experiment can help overcome local obstacles.

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.

Culture supernatants prepared from reactogenic strains of Vibrio cholerae cause a decrease in the transcellular epithelial resistance of T84 intestinal cells. This decrease correlates with the presence of hemagglutinin/ protease but not with the presence of other potential accessory toxins or proteases. These data suggest a possible role for hemagglutinin/protease in reactogenicity, although other factors may also contribute.The potentially life-threatening disease cholera is caused by toxigenic strains of the gram-negative organism Vibrio cholerae. The hallmark symptom of cholera, profuse, watery diarrhea, is caused primarily by cholera toxin (CT). The genes encoding CT, ctxAB, are carried on a transducing phage, CTX⌽, that integrates into the V. cholerae genome (29). The "core" element of the phage genome carries four genes in addition to ctxAB : cep, orfU, ace, and zot (29). Both zot and orfU are known to be essential for phage morphogenesis (29). In addition, the recombinant products of the zot and ace genes have also been associated with changes in intestinal tissue conductance, suggesting that these genes encode accessory toxins of V. cholerae (6,27,28).The development of a safe and effective vaccine to protect against cholera is a multifaceted problem. An ideal cholera vaccine must confer long-lasting protective immunity, be inexpensive, and be easy to use. A vaccine strategy employing live attenuated V. cholerae strains should meet each of these requirements (15, 17). However, production of a safe, attenuated strain has been problematic. Shortly after the discovery of the genes zot and ace, one would have predicted that a core deletion, resulting in mutants unable to produce CT, zonula occludens toxin (Zot), and accessory cholera enterotoxin (Ace), would produce ideal vaccine candidate strains. However, even with the core element deleted, strains CVD110, CVD111, and CVD112 were still "reactogenic," causing residual side effects in volunteer recipients, including mild diarrhea, nausea, vomiting, abdominal cramps, and fever (21, 23). Similarly, vaccine strains with deletions of the entire integrated CTX⌽ element (attRS deletions) are also mildly reactogenic (5, 24). These data indicate that these strains encode additional reactogenic factors encoded at loci other that the integrated CTX⌽ prophage. Curiously, the reactogenic effect of these undefined factors is absent from vaccine candidate strains that have additional defects in motility (5,11,24). This paper describes experiments using transcellular epithelial resistance (TER) across polarized T84 epithelial cells to monitor potential reactogenic factors in various vaccine strains. We show that an activity associated with the zot gene is not detected in this system. However, we find that a decrease in TER correlates with the presence of the genes for production of hemagglutinin/protease (HA/protease), indicating that HA/protease may be a significant contributor to the reactogenicity of some V. cholerae vaccine strains.Addition of supernatant fluids to pol...

Here we briefly review two examples in diverse pathogen-host systems, one well-studied and one newly-dis-