Molecular forensics 2

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Molecular Forensics Adapting a Case for Two Different Course Levels

Transcript of Molecular forensics 2

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Molecular Forensics

Adapting a Case for Two

Different Course Levels

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Molecular Forensics

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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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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

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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

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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

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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

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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/

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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

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Sample Trees

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Clustal WUnrooted Tree

http://Workbench.sdsc.edu

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Clustal WRooted Tree

http://Workbench.sdsc.edu

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Clustal WSequence Alignment

http://Workbench.sdsc.edu

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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

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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