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.

Ribonucleases H from the thermophilic bacterium Thermus thermophilus and the mesophile Escherichia coli demonstrate a dramatic and surprising difference in their change in heat capacity upon unfolding (⌬Cp°). The lower ⌬Cp°of the thermophilic protein directly contributes to its higher thermal denaturation temperature (T m). We propose that this ⌬Cp°difference originates from residual structure in the unfolded state of the thermophilic protein; we verify this hypothesis by using a mutagenic approach. Residual structure in the unfolded state may provide a mechanism for balancing a high T m with the optimal thermodynamic stability for a protein's function. Structure in the unfolded state is shown to differentially affect the thermodynamic profiles of thermophilic and mesophilic proteins.T hermophilic organisms thrive at temperatures where proteins from mesophilic organisms are often completely unfolded and nonfunctional. Understanding the mechanisms by which proteins function at such high temperatures will help to optimize and design thermostable functional proteins for a variety of biotechnological applications. To learn how proteins from thermophilic organisms (thermophilic proteins) function at such elevated temperatures, we need to understand what makes these proteins different from their mesophilic homologs. This difference clearly does not reside in the overall structure of the native conformation; structures of numerous pairs of homologous proteins show that the thermophilic and mesophilic proteins invariably adopt the same fold (1). Examining the differences between individual amino acids and their specific interactions has led to the conclusion that the rules are extremely complex (2, 3).Thermodynamic comparisons of thermophilic and mesophilic pairs of proteins can provide a rational framework for understanding the functional differences between thermophilic and mesophilic proteins. A protein's thermodynamic stability is defined as the difference between the free energies of the native and the unfolded states (⌬G unf ϭ G U Ϫ G N ). The manner in which protein stability depends on temperature is illustrated by the so-called ''protein stability curve,'' which is defined by the Gibbs-Helmholtz equation (4, 5) (for an example, see Fig. 4). The temperature at which the ⌬G unf°e quals zero is the thermal denaturation midpoint (T m ), and the curvature of the stability curve, determined under standard conditions, is given by the heat capacity change upon unfolding (⌬Cp°). There are several ways in which a protein stability curve can be altered to result in a larger T m . An increase in the number of enthalpic interactions will raise the curve and make the protein more stable at every temperature. Alternatively, a lowering of the ⌬Cp°produces a ''flatter'' curve, which results in a higher T m for the same stability maximum. The question then becomes, how do thermophilic proteins alter these protein stability curves and how are they encoded in the structure and sequence?Thermus thermophilus and Escherichia coli RNa...

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.

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