Molecular forensics 2

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  • 1. Molecular Forensics Adapting a Case for Two Different Course Levels
  • 2. Molecular Forensics
  • 3. 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
  • 4. 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
  • 5. 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
  • 6. 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
  • 7. 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
  • 8. 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/
  • 9. 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
  • 10. Sample Trees
  • 11. Clustal WUnrooted Treehttp://Workbench.sdsc.edu
  • 12. Clustal W Rooted Treehttp://Workbench.sdsc.edu
  • 13. Clustal WSequence Alignment http://Workbench.sdsc.edu
  • 14. 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
  • 15. 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