TABLE 1.

Summary of course units, goals, and on-demand assessment

Unit	Title	Concepts	Skills	Sample questions	Assessment
1	Plasmid DNA isolation from E. coli harboring 16S clones	Organization of bacterial DNA and plasmids; Structure and function of 16S rRNA; Chemistry of DNA and proteins; Spectrophotometry of nucleic acids	Use of microbiological media; Column separation and elution; Centrifugation; Calculating DNA concentration	Explain what each of the following reagents does and when it is used: SDS, nuclease-free water, resin, EDTA, and ampicillin. After cell lysis, neutralization, and centrifugation, the genomic DNA is in the pellet but the plasmid is not. Why?	Conceptual Understanding Inquiry Conceptual
2	Restriction analysis of 16S clones	Origin and function of restriction enzymes; Enzyme optima and buffer Restriction fragment length polymorphisms; Principles of agarose gel electrophoresis	Calculating restriction digests; Graphing DNA mobilities; Mapping unknown plasmids; Computerized gel imaging	Using the provided Gibco catalog, determine how many times PinAI would cut a chromosome of 1 million base pairs? You have decided that your insert can only be cut with PinAI. However, your vector lacks this site. What other options do you have to clone your insert into your vector?	Performance Performance Understanding Inquiry
3	DNA sequencing of 16S clones	Principles of DNA replication; Taq polymerases and extremozymes; Chemistry and structure of nucleotides; Principles of acrylamide gel electrophoresis	DNA sequencer operation; PCR operation; Multitasking integrated tasks	Consider the following things that are needed for DNA replication: template, primers, polymerase, and monomers. For each, explain its purpose and compare and contrast what is used for in vitro vs in vivo replication. Compare and contrast gel electrophoresis methods used for restriction analysis with those used for sequence analysis.	Conceptual Conceptual
4	Bioinformatics and phylogenetics	Molecular evolution and chronometers; Structure and significance of 16S rRNA; Taxonomy and diversity of bacteria; Phylogenetic trees as “hypotheses”; Levelsof scientific literature	Computer-based DNA editing; Multiple sequence alignment; Internet-based data retrieval; Computational phylogenetics; Statistical analysis	In order for a molecular phylogeny to reflect organismal phylogeny, what four properties must the molecular data possess? Within the context of your phylogenetics lab exercise, what is your ultimate goal?	Conceptual Understanding Inquiry
5	DNA isolation and cloning of new 16S community libraries	Topoisomerases and ligases in cloning; The lac operon, genetics and applications; Transformation and heat shock response; Organic extractions; Effects of buffer on PCR	Comparative DNA isolation; PCR operation; RFLP-based library screening	Explain how each of the following steps were achieved during genomic isolation: DNA precipitation, separation of DNA, and cell lysis. Discuss specific reagents. The vector that was used to clone PCR product was called pCRTopo/T-A. How does it achieve ligation so efficiently?	Conceptual Conceptual