1. 10Aug2007Jonathan Davies: IISME/CSEE Jonathan Davies West Linn High School West Linn, OR jsdavies@mac.com Mentor : Todd DeSantis Gary Andersen’s Molecular Microbial Ecology Group The PhyloChip A User’s Guide for a 16S Microarray

2. 10Aug2007Jonathan Davies: IISME/CSEE Clinical Research Study the microbial community present in a patient. B. anthracis in lung tissue

3. 10Aug2007Jonathan Davies: IISME/CSEE 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

4. 10Aug2007Jonathan Davies: IISME/CSEE The 16S rRNA Gene It codes for the small subunit of the ribosome A gene found only in prokaryotes It can be species specific

5. 10Aug2007Jonathan Davies: IISME/CSEE Classifying with the 16S Both Start with –DNA Extraction –Polymerase Chain Reaction (PCR) Conventional Method (Greengenes) PhyloChip microarray

6. 10Aug2007Jonathan Davies: IISME/CSEE Conventional Method Gel check for 1.5Kbp Clone the targeted amplicons Send off for sequencing Receive a chromatogram Classify sequences with Greengenes

7. 10Aug2007Jonathan Davies: IISME/CSEE What is Greengenes? 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

8. 10Aug2007Jonathan Davies: IISME/CSEE PhyloChip Procedure All procedures can be completed within the lab. Greatly reduces time needed to get results Detects a broader spectrum in microbial community

9. 10Aug2007Jonathan Davies: IISME/CSEE My role in making technologies accessible Greengenes Tutorial ( summer ‘06 ) Greengenes Updates –Realignment of Tutorial to Greengenes –Addition to Education Lesson Bank PhyloChip User’s Guide

10. 10Aug2007Jonathan Davies: IISME/CSEE 2nd Annual Greengenes Tutorial Researchers –UCSF, UC Berkeley & Stanford Educators –Local biology teachers –Fellow CSEE teachers –Ecology Lesson

11. 10Aug2007Jonathan Davies: IISME/CSEE PhyloChip User’s Guide Compile protocols developed in lab –PCR –Quantitation –Labeling –Hybridizing –Staining –Reading and Analysis

12. 10Aug2007Jonathan Davies: IISME/CSEE PhyloChip User’s Guide Shadowed researchers using PhyloChip Shot Video of the various procedures Technical writing to create a unified flowing document

13. 10Aug2007Jonathan Davies: IISME/CSEE Next Steps: 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

14. 10Aug2007Jonathan Davies: IISME/CSEE Acknowledgements: 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.