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Introducing Bioinformatics Using the Nitrogen Cycle

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

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Introducing Bioinformatics Using the Nitrogen Cycle

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  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 EPASource: http://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

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