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Molecular Forensics

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

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Molecular Forensics

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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 W Unrooted Tree http://Workbench.sdsc.edu

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

  13. Clustal W Sequence 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

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