The%20PhyloChip

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The PhyloChip

• A Users Guide for a 16S Microarray

Jonathan Davies West Linn High School West
Linn, OR jsdavies_at_mac.com
Mentor Todd DeSantis Gary Andersens Molecular
Microbial Ecology Group
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Clinical Research

• Study the microbial community present in a
  patient.

B. anthracis in lung tissue
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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

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The 16S rRNA Gene

• It codes for the small subunit of the ribosome
• A gene found only in prokaryotes
• It can be species specific

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Classifying with the 16S

• Both Start with
• DNA Extraction
• Polymerase Chain Reaction (PCR)
• Conventional Method (Greengenes)
• PhyloChip microarray

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Conventional Method

• Gel check for 1.5Kbp
• Clone the targeted amplicons
• Send off for sequencing
• Receive a chromatogram
• Classify sequences with Greengenes

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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

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PhyloChip Procedure

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

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My role in making technologies accessible

• Greengenes Tutorial (summer 06)
• Greengenes Updates
• Realignment of Tutorial to Greengenes
• Addition to Education Lesson Bank
• PhyloChip Users Guide

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2nd Annual Greengenes Tutorial

• Researchers
• UCSF, UC Berkeley Stanford
• Educators
• Local biology teachers
• Fellow CSEE teachers
• Ecology Lesson

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PhyloChip Users Guide

• Compile protocols developed in lab
• PCR
• Quantitation
• Labeling
• Hybridizing
• Staining
• Reading and Analysis

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PhyloChip Users Guide

• Shadowed researchers using PhyloChip
• Shot Video of the various procedures
• Technical writing to create a unified flowing
  document

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Next Steps

• Field Test the PhyloChip Users Guide
• Curate Additions and Improvements to Greengenes
  Tutorial
• Publish Ecology Lesson to Tutorial
• Collect Data From Teachers Using the Tutorial and
  Lessons

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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.