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

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

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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

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

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