Unit 5 Case Study Handout PDF

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Case study for unit 5 for the class !!!!!!!!!!!...

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Unit 5 Case Study Handout This handout is specific to the case study, Murder by HIV? Some of the questions may require you to some research.

Introductory Reading: Before beginning the case study, learn more about phylogenetic trees and the HIV life cycle.

Case Study Questions: Important: Read through the case study as you answer the questions. There are a couple of changes to the steps in Part III of the case study. You must make these changes, otherwise your phylogenetic tree will be incorrect. These changes can be found in the Murder by HIV PDF but they are included here as well:  

In step 2, you are going to search a nucleotide sequence for patient “AY156807”. In step 10, you will get a list of “hits” that have nucleotide similarities to your Query sequence (from the patient). Click on the first 8 boxes of the victim sequences (e.g., HIV-1 clone V2.MIC.RT) and patient sequences (e.g., HIV-1 clone P6-MIC-RT). You will have a total of 8 boxes checked. You will also select sequences from other sources. To do this, check the boxes for Accession numbers AY835777.1, AF251949.1, FJ030791.1, DQ177231.1. A screenshot of the sequences you must include are below. (The sequence from Belgium will not be in the same location as you see here.) Click “Distance tree of results” once you are done.

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Take a screen shot of your phylogenetic tree. Download the phylogenetic tree and save the PDF to your computer. You will upload this PDF along with this handout. This is worth 10% of the Unit 5 Case Study assignment grade.

To download a PDF of your tree, click on “Tools” -> “Create PDF-file” -> click on the website link.

Questions: 1. You can imagine that the defense team posed alternative means by which the woman could have become infected. What are some other possibilities? List them below. 2. What kinds of tests or information could be used to rule out these alternative hypotheses for her infection with HIV? 3. HIV-1 mutates rapidly. Based on this, would you expect to find a single, identical sequence in the victim and the patient, or would you expect to find a set of related sequences that share a common ancestor? Explain your answer. 4. Include a screenshot of your tree below (even though you are also submitting a PDF of the tree). ---Screenshot of phylogenetic tree--5. Does there appear to be a relationship between the patient and victim sequences? Do they appear to diverge from a common ancestor? Explain your answers using the phylogenetic tree. 6. What conclusion can you draw from this tree? In your answer, use the results in your phylogenetic tree to support your conclusion. 7. Given the circumstantial evidence and the phylogenetic evidence, what do you think the verdict was in this case?...