1 / 6

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

Download Presentation

Introducing Bioinformatics Using the Nitrogen Cycle

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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

More Related