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Molecular Forensics Adapting a Case for Two Different Course Levels

Molecular Forensics Adapting a Case for Two Different Course Levels

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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

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Page 1: Molecular Forensics Adapting a Case for Two Different Course Levels

Molecular Forensics

Adapting a Case for Two

Different Course Levels

Page 2: Molecular Forensics Adapting a Case for Two Different Course Levels

Molecular Forensics

Page 3: Molecular Forensics Adapting a Case for Two Different Course Levels

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

Page 4: Molecular Forensics Adapting a Case for Two Different Course Levels

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

Page 5: Molecular Forensics Adapting a Case for Two Different Course Levels

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

Page 6: Molecular Forensics Adapting a Case for Two Different Course Levels

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

Page 7: Molecular Forensics Adapting a Case for Two Different Course Levels

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

Page 8: Molecular Forensics Adapting a Case for Two Different Course Levels

Tree ModuleWritten Introduction to Trees

Possible ResourcesPhylogenetic TreesSusan CatesThis work is produced by The Connexions Project and licensed under the Creative Commons Attribution Licensehttp://cnx.org/content/m11052/2.8/

Comparing Phylogenetic TreesModule by: sam donovan This work is produced by The Connexions Project and licensed under the Creative Commons Attribution Licensehttp://cnx.org/content/m15807/latest/

Page 9: Molecular Forensics Adapting a Case for Two Different Course Levels

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

Page 10: Molecular Forensics Adapting a Case for Two Different Course Levels

Sample Trees

Page 11: Molecular Forensics Adapting a Case for Two Different Course Levels

Clustal WUnrooted Tree

http://Workbench.sdsc.edu

Page 12: Molecular Forensics Adapting a Case for Two Different Course Levels

Clustal WRooted Tree

http://Workbench.sdsc.edu

Page 13: Molecular Forensics Adapting a Case for Two Different Course Levels

Clustal WSequence Alignment

http://Workbench.sdsc.edu

Page 14: Molecular Forensics Adapting a Case for Two Different Course Levels

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

Page 15: Molecular Forensics Adapting a Case for Two Different Course Levels

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