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 Comparing Phylogenetic Trees Module by: sam donovan This work is produced by The Connexions Project and licensed under the Creative Commons Attribution License
  • 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 Tree
  • 12. Clustal W Rooted Tree
  • 13. Clustal WSequence Alignment
  • 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