The PhyloChip

10Aug2007 Jonathan Davies: IISME/CSEE

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Jonathan Davies West Linn High School

West Linn, [email protected]

Mentor: Todd DeSantisGary Andersen’s Molecular

Microbial Ecology Group

The PhyloChipA User’s Guide for a 16S Microarray




Clinical Research

• Study the microbial community present in a patient.

B. anthracis in lung tissue




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




The 16S rRNA Gene• It codes for the small

subunit of the ribosome• A gene found only in

prokaryotes• It can be species

specific




Classifying with the 16S• Both Start with

– DNA Extraction– Polymerase Chain Reaction (PCR)

• Conventional Method (Greengenes)• PhyloChip microarray




Conventional Method

• Gel check for 1.5Kbp• Clone the targeted

amplicons• Send off for sequencing• Receive a

chromatogram• Classify sequences with

Greengenes




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




PhyloChip Procedure• All procedures can be completed within the lab.• Greatly reduces time needed to get results• Detects a broader spectrum in microbial

community




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




2nd Annual Greengenes Tutorial

• Researchers– UCSF, UC Berkeley &

Stanford• Educators

– Local biology teachers– Fellow CSEE teachers– Ecology Lesson




PhyloChip User’s Guide• Compile protocols developed in lab

– PCR – Quantitation– Labeling– Hybridizing– Staining – Reading and Analysis




PhyloChip User’s Guide• Shadowed researchers using PhyloChip• Shot Video of the various procedures• Technical writing to create a unified

flowing document




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




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.

Documents

The PhyloChip