Presentation on theme: "10Aug2007Jonathan Davies: IISME/CSEE Jonathan Davies West Linn High School West Linn, OR Mentor : Todd DeSantis Gary Andersen’s Molecular."— Presentation transcript:
10Aug2007Jonathan Davies: IISME/CSEE Jonathan Davies West Linn High School West Linn, OR email@example.com Mentor : Todd DeSantis Gary Andersen’s Molecular Microbial Ecology Group The PhyloChip A User’s Guide for a 16S Microarray
10Aug2007Jonathan Davies: IISME/CSEE Clinical Research Study the microbial community present in a patient. B. anthracis in lung tissue
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
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
10Aug2007Jonathan Davies: IISME/CSEE Classifying with the 16S Both Start with –DNA Extraction –Polymerase Chain Reaction (PCR) Conventional Method (Greengenes) PhyloChip microarray
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
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
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
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
10Aug2007Jonathan Davies: IISME/CSEE PhyloChip User’s Guide Compile protocols developed in lab –PCR –Quantitation –Labeling –Hybridizing –Staining –Reading and Analysis
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
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
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.
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