BIOL368/F16:Week 9

This page is currently under construction.

This journal entry is due on Tuesday, November 1 at midnight PDT (Monday night/Tuesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Individual Journal Assignment

• Store this journal entry as "username Week 9" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Link to this assignment from your journal entry.
  • Don't forget to add the "BIOL368/F16" category to the end of your wiki page.

Homework Partners

For your HIV Structure Project, you will be back to working in groups of two. You have the option of working with your partner from the HIV Evolution Project or changing partners. We will take a few moments in class to assemble partners before beginning work this week. Please sit next to your partner in class.

Defining Your HIV Structure Research Project

For this project, you can choose to work with the same sequences you used for the HIV Evolution Project, or you may choose different sequences. You will reframe your question from the HIV Evolution Project to make it a structure→function question. Instead of looking at the evolution of variation of the viral DNA sequences, you will look at how variations in the viral amino acid sequences affect the structure and, therefore, function of the virus.

In this week's journal assignment, you will define your research project by answering the following:

1. What is your question?
2. Make a prediction about the answer to your question before you begin your analysis.
3. Which subjects, visits, and clones will you use to answer your question?
   • You should choose a combination of subjects, visits, and clones that will add up to approximately 50 sequences. You will need about that many sequences to answer a reasonably complex question. However, you cannot use more because the multiple sequence alignment tool cannot handle more than that many sequences.
   • Justify why you chose the subjects, visits, and clones you did.

HIV Structure In-class Activity

1. Convert your DNA sequences into protein sequences.
   • How will you do this? And how will you know that it was done correctly?
   • Alternately, you can obtain the protein sequences from the BEDROCK HIV Problem Space.
2. Perform a multiple sequence alignment on the protein sequences.
   • Are there more or fewer differences between the sequences when you look at the DNA sequences versus the protein sequences?
   • How do you account for this?
3. Which of the procedures from the Week 8 Assignment that you ran on the entire gp120 sequence are applicable to the V3 fragment you are working with now?
   • How are they applicable?
   • In particular, you should perform the secondary structure prediction on the V3 fragment.
4. Download the structure file for the paper we read in journal club from the NCBI Structure Database.
   • Huang et al. (2005) structure 2B4C.
   • You may also be interested in the structures from the other background references:
     • Kwong et al. (1998) structure 1GC1.
     • Stanfield et al. (1999) structure 1F58
     • Stanfield et al. (1999) structure 2F58
5. These files can be opened with the Cn3D software site that is installed on the computers in the lab (this software is free, so you can download it and use it at home, too.) Alternately, you may choose to use the Star Biochem program to do this portion of your work. Answer the following:
   • Find the N-terminus and C-terminus of each polypeptide tertiary structure.
   • Locate all the secondary structure elements. Do these match the predictions you made above?
   • Locate the V3 region and figure out the location of the sequences from your alignment in the structure.
6. Once you have oriented yourself, analyze whether the amino acid changes that you see in the multiple sequence alignment would affect the 3D structure and explain why you think this.
   • Instead of using Cn3D or StarBiochem to do this, you could use the program ConSurf.

Academic Honesty

As discussed in class, each weekly individual journal assignment needs to conclude with an Acknowledgments and References section.

Acknowledgments

In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge (see below).

1. You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. An appropriate statement could be (but is not limited to) the following:
   • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
     • Sign this statement with your wiki signature.
2. Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
3. If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style. If you need to reference content, use your References section (see below).
4. You must also include this statement unless otherwise noted: "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source."

References

• In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
  • data
  • facts
  • images
  • documents, including the scientific literature
• The references in this section should be accompanied by in text citations on your page that refer to these references.
• The references should be formatted according to the APA guidelines.
• For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.

Shared Journal Assignment

• Store your journal entry in the shared BIOL368/F16:Class Journal Week 9 page. If this page does not exist yet, go ahead and create it.
• Link to the shared journal entry from your user page; this should be part of your template.
• Link the shared journal page to this assignment page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL368/F16" category to the end of the wiki page (if someone has not already done so).

Reflection

1. Which project was more interesting to you: studying the evolution of the HIV virus or studying the structure → function relationship? Why?
   • Note that I'm not asking about the tools you used, but the scientific problem studied.
2. What was the best part of working with a partner on this project? What was the worst part? Has this changed since your last project? Why or why not?
3. Besides the scientific conclusion of your project, what have you learned about the process of doing research as a result of this project?