Molecular Forensics

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					Molecular Forensics
    Adapting a Case for Two
     Different Course Levels
Molecular Forensics
Case Summary
   This case is based on a true story
   HIV+ dentist in Florida was accused of
    infecting several patients
   HIV sequences were obtained for the dentist
    and the patients
   The dentist was sued based on the sequence
    evidence
Goals
   Introduce Bioinformatics to students using case-
    based learning

   Suggest methods for upper level undergraduate
    course, e.g. molecular genetics (300), and lower
    level course such as microbiology (200)

   Demonstrate to students that science is evolving
    and tools are evolving…science is not static
Steps for learning
   Introduce the case: Molecular Forensics
   Look at the “printed” data: HIV sequence data
       Explore the difficulties of manually comparing sequences
       Explore options
   Introduce Workbench
       Align sequences
       Pairwise sequence similarities
       Rooted and unrooted trees
Steps for learning – cont.
(In preparation: Module to show students how to
   interpret trees)


   Use module with students to explore how to interpret
    trees
   Analyze the case using new skills and come to a
    conclusion
Tree Module - Overview
   Explanation of phylogenetic trees
       What do they show?
       What don’t they tell you?
       Are there different types of trees? Why?


   Sample trees
       Correlating taxonomy with trees
       Practice in interpreting
Tree Module
    Written Introduction to Trees

  Possible Resources
    Phylogenetic Trees
     Susan Cates
     This work is produced by The Connexions Project and
     licensed under the Creative Commons Attribution License
     http://cnx.org/content/m11052/2.8/



     Comparing Phylogenetic Trees
     Module by: sam donovan
     This work is produced by The Connexions Project and
     licensed under the Creative Commons Attribution License
     http://cnx.org/content/m15807/latest/
Sample Trees
   Provide students with rRNA sequence data
    from a variety of organisms, e.g. –
       Rabbit, frog, fungus and bacteria


   Provide rooted and unrooted trees based on
    this data


   Show students corresponding alignment
Sample Trees
  Clustal W
Unrooted Tree




http://Workbench.sdsc.edu
   Clustal W
  Rooted Tree




http://Workbench.sdsc.edu
     Clustal W
Sequence Alignment




  http://Workbench.sdsc.edu
Taking the Case Farther
   Higher level courses..300 level and higher


       Compare the HIV from the “dentist forensics” case
        with HIV sequences from other studies

       Look at trees and interpret
Taking the Case Further
   Lower level courses: 200 level and below


       Take the rooted and/or unrooted trees produced
        from the case data and create a mobile which
        shows the relationships between samples

				
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posted:10/4/2012
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