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Katie Sandlin

The Genomics Education Partnership: Successful Integration of Research Into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.

Example of a student annotation of a gene. (A) Student-generated gene model (orange) compared with models from various ab initio gene prediction algorithms. Note the first two exons (top left) of the manually generated model, not found in any of the ab initio predictions. (B) Alignment of the amino acids of the first two exons of the gene model from D. melanogaster and the student model from D. erecta.

Shaffer CD, Alvarez C, Bailey C, et al. The Genomics Education Partnership: Successful Integration of Research Into Laboratory Classes at a Diverse Group of Undergraduate Institutions. CBE Life Sci Educ. 2010;9(1):55‐69. doi:10.1187/09-11-0087

Undergraduate Research: Genomics Education Partnership




Abstract: The Genomics Education Partnership offers an inclusive model for undergraduate research experiences incorporated into the academic year science curriculum, with students pooling their work to contribute to international data bases.

A sample of comments by students and teaching assistants on the genomics learning experience.

Lopatto D, Alvarez C, Barnard D, et al. Undergraduate Research. Genomics Education Partnership. Science. 2008;322(5902):684‐685. doi:10.1126/science.1165351

Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains

Abstract:

Background: Chromosome four of Drosophila melanogaster, known as the dot chromosome, is largely heterochromatic, as shown by immunofluorescent staining with antibodies to heterochromatin protein 1 (HP1) and histone H3K9me. In contrast, the absence of HP1 and H3K9me from the dot chromosome in D. virilis suggests that this region is euchromatic. D. virilis diverged from D. melanogaster 40 to 60 million years ago.

Results: Here we describe finished sequencing and analysis of 11 fosmids hybridizing to the dot chromosome of D. virilis (372,650 base-pairs) and seven fosmids from major euchromatic chromosome arms (273,110 base-pairs). Most genes from the dot chromosome of D. melanogaster remain on the dot chromosome in D. virilis, but many inversions have occurred. The dot chromosomes of both species are similar to the major chromosome arms in gene density and coding density, but the dot chromosome genes of both species have larger introns. The D. virilis dot chromosome fosmids have a high repeat density (22.8%), similar to homologous regions of D. melanogaster (26.5%). There are, however, major differences in the representation of repetitive elements. Remnants of DNA transposons make up only 6.3% of the D. virilis dot chromosome fosmids, but 18.4% of the homologous regions from D. melanogaster; DINE-1 and 1360 elements are particularly enriched in D. melanogaster. Euchromatic domains on the major chromosomes in both species have very few DNA transposons (less than 0.4 %).

Conclusion: Combining these results with recent findings about RNAi, we suggest that specific repetitive elements, as well as density, play a role in determining higher-order chromatin packaging.

Repeat analysis of D. virilis contigs compared to the D. melanogaster genome. The repeat density, defined as the percentage of total sequence (in base-pairs) that has been annotated as repetitive has been calculated using the D. virilis fosmid sequence obtained in this study and homologous regions from D. melanogaster (see Materials and methods). D. melanogaster and D. virilis have a very similar low repeat density on the major chromosome arms, and a similar but much higher repeat density on the dot chromosomes. (a) Percent repeat for each type identified by RepeatMasker using RebBase 8.12 with additional repeats identified in a BLASTN all-by-all comparison of the fosmid sequences presented here. (b) Percent repeat for each type identified by RepeatMasker using the Superlibrary (see text for description). The dot chromosome of D. melanogaster has about three times more DNA transposon sequence than does the D. virilis dot chromosome. 'Unknown' repeats are those from both RebBase 8.12 and the D. virilis PILER-DF library that have not been classified as to type.

Slawson EE, Shaffer CD, Malone CD, et al. Comparison of Dot Chromosome Sequences from D. melanogaster and D. virilis Reveals an Enrichment of DNA Transposon Sequences in Heterochromatic Domains. Genome Biol. 2006;7(2):R15. doi:10.1186/gb-2006-7-2-r15