Honors Theses


Thomas M. Williams



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Document Type

Honors Thesis


Genomes encode in DNA sequences the recipes for cellular products, notably proteins, and the switches that determine when during life and in which cell types these products are made. While the genetic code for protein recipes is known, a comparable code for these switches is lacking. This impedes understanding the genetic underpinnings of animals and their evolution, as switches (CREs) outnumber protein-coding genes by over an order of magnitude and switch evolution is thought to be a predominant mechanism of trait evolution. Both in vivo and in silico approaches exist to study CREs, but the former is low throughput, and the latter lacks validation of predictions. My research merged these approaches to identify CREs controlling genes for an evolving fruit fly pigmentation trait. I used sequences of CREs known to activate genes involved in pigmentation in order to find the unknown CREs with similar activity. Here I report on the use of the SCRMshaw bioinformatic tool to find putative CREs in the Drosophila melanogaster genome that control novel genes involved in pigmentation, based upon the putative CREs possessing DNA motifs similar to those within the known CREs. From this list, I tested eighteen for CRE activity in vivo as reporter transgenes. As a control, I tested a set of four randomly selected sequences of similar length and deoxyribonucleotide composition for in vivo activity. The results support that this in silico method succeeded in CRE identification. For the validated CREs, future studies can elucidate the molecular mechanisms by which they similarly control gene expression, and whether they evolved in route to the gain, loss, and modification of male-specific abdomen pigmentation. The encoding of information in CREs is a universal feature of life, so these results bear upon life at every level.

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Undergraduate research

Embargoed until Sunday, June 23, 2120