BIOL368/F16:Week 8

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This journal entry is due on Tuesday, October 25 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.

Background for HIV Structure Project

• BEDROCK HIV Problem Space
  • Amino Acid Sequence Data
• HIV Database at Los Alamos National Laboratory
• StarBiochem
• Download NCBI Cn3D
• NCBI Structure Database

References

Reviews

• Merk, A., & Subramaniam, S. (2013). HIV-1 envelope glycoprotein structure. Current opinion in structural biology, 23(2), 268-276. DOI: 10.1016/j.sbi.2013.03.007
• Turner, B. G., & Summers, M. F. (1999). Structural biology of HIV. Journal of molecular biology, 285(1), 1-32. DOI: 10.1006/jmbi.1998.2354

Primary Research Articles for Journal Club

• Andrianov, A. M., & Anishchenko, I. V. (2009). Computational model of the HIV-1 subtype A V3 loop: Study on the conformational mobility for structure-based anti-AIDS drug design. Journal of Biomolecular Structure and Dynamics, 27(2), 179-193. DOI: 10.1080/07391102.2009.10507308
• Kirchherr, J. L., Hamilton, J., Lu, X., Gnanakaran, S., Muldoon, M., Daniels, M., ... & Musonda, R. M. (2011). Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120. Virology, 409(2), 163-174. DOI: 10.1016/j.virol.2010.09.031
• Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (1998). Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature, 393(6686), 648-659. DOI: 10.1038/31405

Individual Journal Assignment

• Store this journal entry as "username Week 8" (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.

Preparation for Week 9 Journal Club

For this assignment, you will work both individually and as a group of four. Individually, you will make your own outline and list of definitions of the journal article. As a group, you will prepare a PowerPoint presentation and present it next week in class.

In preparation for the Journal Club, each individual will do the following assignment on their individual Week 8 Journal page.

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own URL citation.
2. Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
   • What is the main result (message) presented in this paper?
   • What is the importance or significance of this work?
   • What were the limitations in previous studies that led them to perform this work?
   • What were the methods used in the study?
   • Briefly state the result shown in each of the figures and tables.
   • How do the results of this study compare to the results of previous studies.
3. This time your group will prepare the PowerPoint slides for your Journal Club Presentation.
   • Include the following slides:
     • Title slide with the full citation of the journal article in APA format (authors, year, title, journal name, volume, page numbers, DOI) the names of the presenting group members, the date, and the class number and title.
     • Outline slide
     • Introduction slide(s) to HIV
     • A slide for every figure and table in the paper with an explanatory title that is a phrase or sentence that explains the main point of the figure/table.
     • One or more slides based on the Discussion and summarizing the paper (your outline slide can become your summary if reworded properly.
   • Upload your slides to the OpenWetWare wiki by the Week 8 journal assignment deadline. Each member of your group should have a link to the same PowerPoint file. You may make changes to your slides in advance of your presentation, but you will be graded on what you upload by the journal deadline.
     • Use these Presentation Guidelines when preparing your PowerPoint slides.
     • Your presentation will also be graded on the following Presentation Rubric.

Note: The individual journal entry for this week is worth 10 points like all other journal entries. The journal club presentation is worth 35 points. The same presentation grade will be given to the entire group.

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 8 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. After working with the protein tools on today's assignment, compare your experience with working with the nucleic acid tools versus the protein tools. Which do you like better, and why?