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The PhyloChip

The PhyloChip. A User’s Guide for a 16S Microarray. Jonathan Davies West Linn High School West Linn, OR jsdavies@mac.com. Mentor : Todd DeSantis Gary Andersen’s Molecular Microbial Ecology Group. Clinical Research. Study the microbial community present in a patient.

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The PhyloChip

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  1. The PhyloChip A User’s Guide for a 16S Microarray Jonathan Davies West Linn High School West Linn, OR jsdavies@mac.com Mentor: Todd DeSantis Gary Andersen’s Molecular Microbial Ecology Group Jonathan Davies: IISME/CSEE

  2. Clinical Research • Study the microbial community present in a patient. B. anthracis in lung tissue Jonathan Davies: IISME/CSEE

  3. Environmental Microbiology • To monitor the effectiveness of bioremediation efforts • To compare the microbial communities from different locales • To see how a microbial community changes over time Jonathan Davies: IISME/CSEE

  4. It codes for the small subunit of the ribosome A gene found only in prokaryotes It can be species specific The 16S rRNA Gene Jonathan Davies: IISME/CSEE

  5. Both Start with DNA Extraction Polymerase Chain Reaction (PCR) Conventional Method (Greengenes) PhyloChip microarray Classifying with the 16S Jonathan Davies: IISME/CSEE

  6. Conventional Method • Gel check for 1.5Kbp • Clone the targeted amplicons • Send off for sequencing • Receive a chromatogram • Classify sequences with Greengenes Jonathan Davies: IISME/CSEE

  7. An up-to-date database of known 16S rRNA gene sequences A web based tool used to classify cloned bacterial DNA sequences Allows users to compare sequences to each other and to landmarks in the Greengenes database What is Greengenes? Jonathan Davies: IISME/CSEE

  8. PhyloChip Procedure • All procedures can be completed within the lab. • Greatly reduces time needed to get results • Detects a broader spectrum in microbial community Jonathan Davies: IISME/CSEE

  9. Greengenes Tutorial (summer ‘06) Greengenes Updates Realignment of Tutorial to Greengenes Addition to Education Lesson Bank PhyloChip User’s Guide My role in making technologies accessible Jonathan Davies: IISME/CSEE

  10. 2nd Annual Greengenes Tutorial • Researchers • UCSF, UC Berkeley & Stanford • Educators • Local biology teachers • Fellow CSEE teachers • Ecology Lesson Jonathan Davies: IISME/CSEE

  11. Compile protocols developed in lab PCR Quantitation Labeling Hybridizing Staining Reading and Analysis PhyloChip User’s Guide Jonathan Davies: IISME/CSEE

  12. Shadowed researchers using PhyloChip Shot Video of the various procedures Technical writing to create a unified flowing document PhyloChip User’s Guide Jonathan Davies: IISME/CSEE

  13. Field Test the PhyloChip User’s Guide Curate Additions and Improvements to Greengenes Tutorial Publish Ecology Lesson to Tutorial Collect Data From Teachers Using the Tutorial and Lessons Next Steps: Jonathan Davies: IISME/CSEE

  14. Todd DeSantis Gary Andersen Eoin Brodie Yvette Piceno CSEE: Laurel Egenberger, Rollie Otto, Michael Thibodeau,Tom Knight, & Joe Crippen IISME: Jennifer Bruckner, Patti Forster & Kaye Storm Stephen D. Bechtel Jr. Acknowledgements: Jonathan Davies: IISME/CSEE

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