Table 8.

Student responses to the following question: “Imagine you are a genomicist working for CDC and there has been an outbreak of enterohemorrhagic disease that has resulted in illness of 100,000 people and deaths of 1000 of those patients, making this the most deadly outbreak of E. coli that has ever been reported. Bacteria cultured from the fecal material of some of the patients all revealed the same strain of E. coli that had never before been described. You have funds to sequence the genome of this strain. Design a bioinformatic study in which you approach the challenge of determining which genes might be contributing to the extreme virulence of this strain.”

Criteria	Student response	% (n = 36)
Biology
1. Student can define and describe the concept of a virulence factor, and briefly describe at least two classes of genes that function as virulence factors.	Provided a complete, well-reasoned, answer	66.7
		Provided an incomplete/superficial answer	27.8
	Did not address this topic	5.5
2. Student can define the evolution, structure, and function of pathogenicity islands.	Provided a complete, well-reasoned, answer	61.1
		Provided an incomplete/superficial answer	30.6
	Did not address this topic	8.3
Bioinformatics
3. Student can explain that a comparison of genome sequences between closely related strains of E. coli will reveal genomic islands unique to one or more strains, and these may represent pathogenicity islands.	Provided a complete, well-reasoned, answer	69.4
		Provided an incomplete/superficial answer	27.8
	Did not address this topic	2.8
4. Student can describe a bioinformatics approach to identify genomic islands.	Provided a complete, well-reasoned, answer	72.2
		Provided an incomplete/superficial answer	27.8
	Did not address this topic	0.0
5. Student can describe a bioinformatics approach to learn about the potential functions of genes located within the genomic island.	Provided a complete, well-reasoned, answer	50.0
		Provided an incomplete/superficial answer	41.7
	Did not address this topic	8.3
Experimental process
6. Student understands that experimental verification is needed to demonstrate that one or more of the genes contained within an island might function as virulence factors	Provided a complete, well-reasoned, answer	38.9
		Provided an incomplete/superficial answer	25.0
	Did not address this topic	36.1