1. Introducing Bioinformatics Using the Nitrogen Cycle Alyssa Bumbaugh Ron Peck Mark Radosevich

2. Goals Use bioinformatics to provide a “course capstone” to integrate sequence, structure, and function along with ecology and metabolism in an introductory biology or soils course Discussion/Introduction of key terms or concepts – Genes, protein structure and function, molecular biology research tools (PCR, etc), ecology, metabolic pathways Student use of Biology Workbench – Gene/protein searches – Alignment tools

3. Courtesy EPA Source: http://www.epa.gov/maia/html/nitrogen.htmlhttp://www.epa.gov/maia/html/nitrogen.html

4. Class Time Instruction Demonstration of Biology Workbench or NCBI for BLAST searches Lecture discussion of phylogenetic trees – Universal tree of life Lecture discussions of metabolic pathways – Nitrogen, specifically the nitrification process – Universal metabolic pathway such as glycolysis Lecture discussion of protein structure and function Lecture on microbial diversity/ecology – Habitats, growth substrates

5. Questions Posed to the Students What is the length of the protein sequence? the nucleotide sequence? – Students will explore how nucleic acids relate to proteins How widely distributed is ammonia monooxygenase in prokaryotes? – Search for: Ammonia monooxygenase AND NOT (complete) – Students will need to report the genera, habitat Google or The Prokaryotes for this information

6. Questions Posed to the Students How does the distribution compare with the tree of life? – Students will need to align sequences and build tree A comparison will be made to a universal pathway enzyme (enolase) What are the other enzymes in this pathway? – Use of the KEGG database What differences exist between the sequences of isolates found in different habitats? – Compare soil and aquatic isolates