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ASM/JGI Bioinformatics Institute

ASM/JGI Bioinformatics Institute. Ellen Aho Concordia College Moorhead Minnesota. Research students Upper-level microbiology students Introductory-level genetics students. Research students: Neisseria meningitidis gene curation.

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ASM/JGI Bioinformatics Institute

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  1. ASM/JGI Bioinformatics Institute Ellen Aho Concordia College Moorhead Minnesota

  2. Research students • Upper-level microbiology students • Introductory-level genetics students

  3. Research students:Neisseriameningitidisgene curation BIGSdb: Scalable analysis of bacterial genome variation at the population level Keith A Jolley and Martin CJ Maiden • BMC Bioinformatics 2010, 11:595 >pilS1 DIKGKYVKEVKVANGVITATMLSSGVNNEIKGKKLSLWAKRQNGSVKWFCGQPVARADKAKDDVKAATANGTDDKINTKHLPSTCRDDSS http://www3.imperial.ac.uk

  4. Research students • Building confidence • Student training resources • Data management ideas • Alignment tools

  5. Microbiology students:commensalNeisseria genomes • Genome sequencing reveals widespread virulence gene exchange among human Neisseria species Marri et al. • PLoS One 2010, 5:e11835

  6. Microbiology students • IMG-ACT workshop • Identify interesting questions and multiple places to integrate into syllabus • Identify tools and begin to design assignments

  7. Microbiology students • 1. Introduction to Neisseria • N. meningitidiscomparative genomics article • Review of NCBI, introduction to IMG: find genomes of different • meningococcal serogroups • Phylogenetic profiler: comparisons amongst meningococci – • open genome, pangenome • Lab time during bacterial genetics/antibiotic resistance section of class • Antibiotic resistance gene via HGT article • Introduction to commensal genomes • Retrieve gene(s), BLAST all commensals • HGT analyses 3. During vaccine section: group projects – research candidate vaccine antigens • Students find articles about neisserial vaccine development • Make class list of candidate antigens • Groups investigate a given candidate antigen • Would a vaccine that elicits an immune response against this meningococcal antigen be likely to affect normal flora?

  8. Group projects • Normal function of candidate antigen • Find N. meningitidisgene in database • Cell location tools • BLAST commensal genomes • MUSCLE alignments of protein sequences, WebLogo • Class poster session

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