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Adding a Bioinformatics Component to the Unknown Project of a Microbiology Course

Adding a Bioinformatics Component to the Unknown Project of a Microbiology Course. Dinene Crater, High Point University Andrew Pease, Stevenson University. Overview of Current Unknown Procedure. Preliminary exercises teaching each biochemical test.

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Adding a Bioinformatics Component to the Unknown Project of a Microbiology Course

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  1. Adding a Bioinformatics Component to the Unknown Project of a Microbiology Course Dinene Crater, High Point University Andrew Pease, Stevenson University

  2. Overview of Current Unknown Procedure Preliminary exercises teaching each biochemical test. Give a list of organisms that will be used as possible unknowns. Give the students 2 unknowns (one gram positive and one gram negative). Students will need to identify their organisms based on the results of the biochemical test and Gram reaction.

  3. List of Organisms • Gram Positive • Staphylococcus aureus • Staphylococcus epidermidis • Bacillus cereus • Enterococcusfaecalis • Gram Negative • Proteus vulgaris • Pseudomonas aeruginosa • Salmonella typhimurium • Klebsiellapneumoniae • Enterobacteraerogenes • Escherichia coli

  4. Overview of ProposedUnknown Procedure • Preliminary exercises teaching each biochemical test. • Incorporate the Bioinformatics learning module. • Give a list of organisms that will be used as possible unknowns. • Give the students 2 unknowns (one gram positive and one gram negative). • Students will need to identify their organisms based on the results of the biochemical test and Gram reaction. • Students will use bioinformatics tools to place their organisms (G+ or G-) into a known phylogenetic tree for a cell wall synthesis enzyme (MraY, phospho-N-acetylmuramoyl-pentapeptide- transferase ).

  5. Bioinformatics Learning Module • Show the final output of the phylogenetic tree for MraY. • Walk students through the process using the bioinoformatics tools. • Tools will include: • IMG of JGI • FASTA • MEGA to align sequences and develop a phylogenetic tree

  6. Learning Module http://img.jgi.doe.gov/edu “Find genes” Type “phospho-N-acetylmuramoyl-pentapeptide- transferase” into the search box. (space matters) Find your organism with the search window.

  7. Learning Module (cont.) • Scroll around the screen to find out several pieces of information on the protein • Size of the protein • Neighboring genes on the chromosome • Aligning the gene with other organisms • Click on the Accession Number to bring it to the NCBI format. • Get the FASTA format from the Display and send to Text. • Copy and paste to the original list.

  8. Learning Module (cont.) • Scroll around the screen to find out several pieces of information on the protein • Size of the protein • Neighboring genes on the chromosome • Click on the Accession Number to bring it to the NCBI format. • Get the FASTA format from the Display and send to Text. • Copy and paste to the original list.

  9. FASTA Format >637785561 MNRLKKSHRQKSLFWRPIAPNPRWQKENPTAHGSTDTGGFGYNGGNEEVK TSSTMMNGIHALVNERQNEWLRGYEVDIKSRFDNIESVLKDILAQQSQLN FVSWANQQLFAKLGVSLTEQDWQSGVQLQSQKGFQFLYGKTLFAQFMRMS EDFFVNDPLSGQRKQEAERMFKEAGFHAVGIAPCADGRLAHILSYVLRLP YALARRKAHAGVMFDVSESVRNWVFIEHTRFRDGQPNLADEPTRYLKIAV YHFSKADPTHQGCAAHGSDDHKAAQAALQKLKDFKQAIENRFGCGSTVQT LLLGLNTDDDSMKVHIPNASGEVCLDRYVETEQLYQATMNLPDSEAKQAL ENAIVTCNQALGSTAPQPELVKLLSWLIGNNFSQIAYVNQYENGCYSDIG HAERFIGIGNGFEEVQLRNLSYYSFLDTVEEGVNDVDVGIKIFKGLNVKK GLPIPIIIRCDYDGRVPGSKDRAEAKALRIEKALHNRYQELSAPGLLQTL PTLRDFTSCKPAERLPGLADLSAKQRTA

  10. List of Sequences for FASTA The students will be provided the list of FASTA sequences for MraY for 24 random bacterial organisms (created by Brad Goodner) They will add their FASTA sequences (from their identified G+ and G-) to the master list (final=26 sequences). The entire list will then be used to create an alignment and phylogenetic tree via MEGA.

  11. Potential Learning Outcomes Students will gain exposure to a variety of bioinformatics tools to search protein databases. Students will learn how to align protein sequences and create phylogenetictrees. Students will enhance their knowledge of genetic diversity between G+ and G- organisms using a common protein.

  12. Useful Websites http://img.jgi.doe.gov/edu http://www.ncbi.nlm.nih.gov http://www.megasoftware.net

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