BIOL368/F11:HIV Structure

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(Week 9)
 
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'''''NOTE:  This page is under construction.'''''
 
== Background ==
== Background ==
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=== References ===
=== References ===
-
<biblio>
+
# 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'' 393:648-659. [http://www.ncbi.nlm.nih.gov/pubmed?term=9641677 PubMed] [http://www.nature.com/nature/journal/v393/n6686/full/393648a0.html Full text]
-
#Paper1 pmid=9641677
+
# Stanfield, R., Cabezas, E., Satterthwait, A., Stura, E., Profy, A., Wilson, I. (1999) Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs.  ''Structure'' 7:131-142 [http://www.ncbi.nlm.nih.gov/pubmed?term=10368281 PubMed] [http://tinyurl.com/Stanfield1999 Full text]
-
//[http://www.nature.com/nature/journal/v393/n6686/full/393648a0.html Kwong et al. (1998) link to full text]
+
# Stanfield RL, Ghiara JB, Ollmann Saphire E, Profy AT, Wilson IA. (2003) Recurring conformation of the human immunodeficiency virus type 1 gp120 V3 loop. ''Virology'' 315:159-173. [http://www.ncbi.nlm.nih.gov/pubmed?term=14592768 PubMed] [http://tinyurl.com/yjpgvpx Full text]
-
#Paper2 pmid=10368281
+
-
//[http://tinyurl.com/Stanfield1999 Stanfield et al. (1999) link to full text]
+
-
#Paper3 pmid=14592768
+
-
//[http://tinyurl.com/yjpgvpx Stanfield et al. (2003) link to full text]
+
-
 
+
-
</biblio>
+
== Week 7 ==
== Week 7 ==
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The class will be divided into groups of 3 or 4. Each group will create and present a Journal Club (in class in Week 8) on the Kwong et al. (1998), Stanfield et al. (1999), or Stanfield et al. (2003) articles.  The groups will be:
The class will be divided into groups of 3 or 4. Each group will create and present a Journal Club (in class in Week 8) on the Kwong et al. (1998), Stanfield et al. (1999), or Stanfield et al. (2003) articles.  The groups will be:
-
* Kwong et al. (1998):  
+
* Kwong et al. (1998): Nicki, Samantha, Zeb
-
* Stanfield et al. (1999):  
+
* Stanfield et al. (1999): Alex, Chris
-
* Stanfield et al. (2003):  
+
* Stanfield et al. (2003): Isaiah, Robert
In preparation for the Journal Club, each individual will do the following assignment on their individual [[BIOL368/F11:Week 7 | Week 7 Journal page]].
In preparation for the Journal Club, each individual will do the following assignment on their individual [[BIOL368/F11:Week 7 | Week 7 Journal page]].
-
# 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).  List the citation(s) for the dictionary(s) you use, providing a URL to the page is fine.
+
# 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).  List the citation(s) for the dictionary(s) you use, providing a URL to the page, along with the date accessed is fine.
-
# Write an outline of the article.  The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper.  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.
+
# Write an outline of the article.  The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (use the "Print Preview" menu item in your browser to check your 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 presented in this paper?  (Hint:  look at the last sentence of the introduction and restate it in plain English.)
#*What is the main result presented in this paper?  (Hint:  look at the last sentence of the introduction and restate it in plain English.)
#*What is the importance or significance of this work?
#*What is the importance or significance of this work?
Line 47: Line 39:
#*What were the methods used in the study?
#*What were the methods used in the study?
#*Briefly state the result shown in each of the figures and tables.
#*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 (See Discussion).
+
#*How do the results of this study compare to the results of previous studies (Include an outline of the Discussion).
 +
# 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: authors, year, title, journal name, volume, page numbers, the names of the 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 7 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 [[Media:PresentationGuidelines.ppt‎ | Presentation Guidelines]] when preparing your PowerPoint slides.
 +
#** Your presentation will also be graded on the following [[Media:PresentationCritiques.pdf | Guide to critiquing talks]].
== Week 8 ==
== Week 8 ==
Line 56: Line 58:
* This week we will begin to learn how to analyze protein structures.  For today, we will be using the ''Bioinformatics for Dummies'' book extensively, so be sure to bring it to class. We will be using some bioinformatics tools to analyze the structure of the gp120 envelope protein.
* This week we will begin to learn how to analyze protein structures.  For today, we will be using the ''Bioinformatics for Dummies'' book extensively, so be sure to bring it to class. We will be using some bioinformatics tools to analyze the structure of the gp120 envelope protein.
-
* Chapter 2:  Retrieving Protein Sequences/Retrieving a list of Related protein sequences (pp. 42-51 in second edition).  The example worked through in the book uses the sequence of an enzyme called dUTPase.  Follow the book example yourself and then work through the example again, this time using the HIV gp120 envelope protein instead.
+
* Chapter 2:  Retrieving Protein Sequences/Retrieving a list of Related protein sequences (pp. 42-51 in second edition).  The example worked through in the book uses the sequence of an enzyme called dUTPase.  Follow the book example yourself, but instead of investigating dUTPase, use the HIV gp120 envelope protein instead.
-
* Chapter 4: Reading a SWISS-PROT entry (pp. 110-123 in the second edition).  The example worked through in the book is the epidermal growth factor receptor.  Work through this example and then do it again with the HIV gp120 envelope protein instead.
+
* Chapter 4: Reading a SWISS-PROT entry (pp. 110-123 in the second edition).  The example worked through in the book is the epidermal growth factor receptor.  Work through this example using the HIV gp120 envelope protein instead.
* Chapter 5: ORFing your DNA sequence (pp. 146-147 in second edition).  In the previous section of the course, we were working with DNA sequences from the HIV gp120 envelope protein.  Take one of your DNA sequences and follow the instructions to find the open reading frames in the sequence.  Since you were working with just a portion of the entire envelope protein, you may get some strange results.  Compare your results with the SWISS-PROT entry you found for the protein above to decipher what the output means.  Besides the NCBI Open Reading Frame Finder described in the book, ExPASy also has a translation tool you can use, found [http://www.expasy.org/tools/dna.html here].
* Chapter 5: ORFing your DNA sequence (pp. 146-147 in second edition).  In the previous section of the course, we were working with DNA sequences from the HIV gp120 envelope protein.  Take one of your DNA sequences and follow the instructions to find the open reading frames in the sequence.  Since you were working with just a portion of the entire envelope protein, you may get some strange results.  Compare your results with the SWISS-PROT entry you found for the protein above to decipher what the output means.  Besides the NCBI Open Reading Frame Finder described in the book, ExPASy also has a translation tool you can use, found [http://www.expasy.org/tools/dna.html here].
* Chapter 6: Working with a single protein sequence (pp. 159-195 in second edition).  Work through the following examples in this chapter using the entire HIV gp120 envelop protein sequence that you obtained from SWISS-PROT.  We will then compare the results of these analyses with the actual structure of the gp120 protein obtained by X-ray crystallography.
* Chapter 6: Working with a single protein sequence (pp. 159-195 in second edition).  Work through the following examples in this chapter using the entire HIV gp120 envelop protein sequence that you obtained from SWISS-PROT.  We will then compare the results of these analyses with the actual structure of the gp120 protein obtained by X-ray crystallography.
Line 67: Line 69:
Today you will begin your HIV gp120 Structure Research Project.
Today you will begin your HIV gp120 Structure Research Project.
-
* For this project, you can choose to work with the same sequences you used for the [[BIOL368/F11:HIV Evolution | 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 how the evolution of variation of the viral DNA sequence affects the different patient groups, you will look at how variations in the viral sequence affect the structure and, therefore, function of the virus.  To answer your question, you will need to do the following:
+
* For this project, you can choose to work with the same sequences you used for the [[BIOL368/F11:HIV Evolution | 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 how the evolution of variation of the viral DNA sequence affects the different patient groups, you will look at how variations in the viral sequence affect the structure and, therefore, function of the virus.  '''''For this week's journal assignment, you must indicate the question that you will study for your project and which data you will use (patients, visits).  Justify your selection of patients and visits. '''''
 +
 
 +
== Week 9 ==
 +
 
 +
To answer your question, you will need to do the following:
# Convert your DNA sequences into protein sequences.   
# Convert your DNA sequences into protein sequences.   
#* How will you do this?   
#* How will you do this?   
Line 76: Line 82:
# Which of the procedures from Chapter 6 that you ran on the entire gp120 sequence are applicable to the V3 fragment you are working with now?   
# Which of the procedures from Chapter 6 that you ran on the entire gp120 sequence are applicable to the V3 fragment you are working with now?   
#* How are they applicable?
#* How are they applicable?
-
# Chapter 11 contains procedures to use for working with protein 3D structures.  Find the section on "Predicting the Secondary Structure of a Protein Sequence" and perform this on both the entire gp120 sequence and on the V3 fragment that we are now working with.  You will compare the predictions with the actual structures.
+
# Chapter 11 contains procedures to use for working with protein 3D structures.  Find the section on "Predicting the Secondary Structure of a Protein Sequence" and perform this on both the entire gp120 sequence and on the V3 fragment that we are now working with.  You will compare the predictions with the actual structures. Use this link to do the prediction, [http://bioinf.cs.ucl.ac.uk/psipred/ ]
# Download the structure files for the papers we read in journal club from the [http://www.ncbi.nlm.nih.gov/sites/entrez?db=Structure&itool=toolbar NCBI Structure Database].
# Download the structure files for the papers we read in journal club from the [http://www.ncbi.nlm.nih.gov/sites/entrez?db=Structure&itool=toolbar NCBI Structure Database].
#* [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=8099 Kwong et al. (1998) structure 1GC1].
#* [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=8099 Kwong et al. (1998) structure 1GC1].
Line 82: Line 88:
#* [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=12087 Stanfield et al. (1999) structure 2F58]
#* [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=12087 Stanfield et al. (1999) structure 2F58]
#* [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=25248 Stanfield et al. (2003) structure 1NAK]
#* [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=25248 Stanfield et al. (2003) structure 1NAK]
-
# These files can be opened with the [http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml 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.)  Familiarize yourself with the software features (rendering and coloring) with both the gp120 peptide and ternary complex structures.  (The ''Dummies'' book has some information on this program as well).  Answer the following:
+
# These files can be opened with the [http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml 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.)  Familiarize yourself with the software features (rendering and coloring) with both the gp120 peptide and ternary complex structures.  Alternately, you may choose to use the [http://web.mit.edu/star/biochem/ Star Biochem] program to do this portion of your work.  Answer the following:
#* Find the N-terminus and C-terminus of each (poly)peptide structure.
#* Find the N-terminus and C-terminus of each (poly)peptide structure.
#* Locate all the secondary structure elements.  Do these match the predictions you made above?
#* Locate all the secondary structure elements.  Do these match the predictions you made above?
Line 88: Line 94:
# 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.
# 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.
# The journal club papers we read are quite old already for a fast-moving field.  Using the [http://0-apps.isiknowledge.com.linus.lmu.edu/ Web of Science] (or [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] or [http://www.ncbi.nlm.nih.gov/sites/entrez?db=Structure&itool=toolbar Structure]) databases, find at least one more recent publication that has a structure of gp120 (V3) in it and download the structure file to view.  What additional information has been learned from this new paper?
# The journal club papers we read are quite old already for a fast-moving field.  Using the [http://0-apps.isiknowledge.com.linus.lmu.edu/ Web of Science] (or [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] or [http://www.ncbi.nlm.nih.gov/sites/entrez?db=Structure&itool=toolbar Structure]) databases, find at least one more recent publication that has a structure of gp120 (V3) in it and download the structure file to view.  What additional information has been learned from this new paper?
-
# Your presentation will be formatted similarly to the previous [[BIOL368/F11:HIV Evolution | HIV Evolution Project]].  In this case, you will want to work on creating structure figures that illustrate what result you are trying to show.
+
# Your presentation for Week 10 will be formatted similarly to the previous [[BIOL368/F11:HIV Evolution | HIV Evolution Project]].  In this case, you will want to work on creating structure figures that illustrate what result you are trying to show.
-
 
+
#* Your presentation will be 15 minutes long (approximately 15 slides, one per minute).  Include:
-
== Week 9 ==
+
#** Title slide
-
 
+
#** Outline slide
-
* Project work session
+
#** Background that led you to ask your research question
-
* Prepare for Project presentations in Week 10
+
#** Your question
 +
#** How you answered your question, method/results
 +
#** Interpretation of your results; answer to your question
 +
#** Discussion and interprettion of your results in light of the new paper you found.
 +
#* Upload your slides to the OpenWetware wiki by the Week 9 journal assignment deadline.  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 [[Media:PresentationGuidelines.ppt‎ | Presentation Guidelines]] when preparing your PowerPoint slides.
 +
#** Your presentation will also be graded on the following [[Media:PresentationCritiques.pdf | Guide to critiquing talks]].
== Week 10 ==
== Week 10 ==

Current revision

BIOL368: Bioinformatics Laboratory

Loyola Marymount University

Home       People        HIV Evolution       HIV Structure       DNA Microarrays       Lionshare       Help  

Contents

Background

References

  1. 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 393:648-659. PubMed Full text
  2. Stanfield, R., Cabezas, E., Satterthwait, A., Stura, E., Profy, A., Wilson, I. (1999) Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs. Structure 7:131-142 PubMed Full text
  3. Stanfield RL, Ghiara JB, Ollmann Saphire E, Profy AT, Wilson IA. (2003) Recurring conformation of the human immunodeficiency virus type 1 gp120 V3 loop. Virology 315:159-173. PubMed Full text

Week 7

Preparation for Week 8 Journal Club

The class will be divided into groups of 3 or 4. Each group will create and present a Journal Club (in class in Week 8) on the Kwong et al. (1998), Stanfield et al. (1999), or Stanfield et al. (2003) articles. The groups will be:

  • Kwong et al. (1998): Nicki, Samantha, Zeb
  • Stanfield et al. (1999): Alex, Chris
  • Stanfield et al. (2003): Isaiah, Robert

In preparation for the Journal Club, each individual will do the following assignment on their individual Week 7 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). List the citation(s) for the dictionary(s) you use, providing a URL to the page, along with the date accessed is fine.
  2. Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (use the "Print Preview" menu item in your browser to check your 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 presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)
    • 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 (Include an outline of the Discussion).
  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: authors, year, title, journal name, volume, page numbers, the names of the 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 7 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.

Week 8

  • Journal Club presentations in class.

Working with Protein Sequences In-class Activity

  • This week we will begin to learn how to analyze protein structures. For today, we will be using the Bioinformatics for Dummies book extensively, so be sure to bring it to class. We will be using some bioinformatics tools to analyze the structure of the gp120 envelope protein.
  • Chapter 2: Retrieving Protein Sequences/Retrieving a list of Related protein sequences (pp. 42-51 in second edition). The example worked through in the book uses the sequence of an enzyme called dUTPase. Follow the book example yourself, but instead of investigating dUTPase, use the HIV gp120 envelope protein instead.
  • Chapter 4: Reading a SWISS-PROT entry (pp. 110-123 in the second edition). The example worked through in the book is the epidermal growth factor receptor. Work through this example using the HIV gp120 envelope protein instead.
  • Chapter 5: ORFing your DNA sequence (pp. 146-147 in second edition). In the previous section of the course, we were working with DNA sequences from the HIV gp120 envelope protein. Take one of your DNA sequences and follow the instructions to find the open reading frames in the sequence. Since you were working with just a portion of the entire envelope protein, you may get some strange results. Compare your results with the SWISS-PROT entry you found for the protein above to decipher what the output means. Besides the NCBI Open Reading Frame Finder described in the book, ExPASy also has a translation tool you can use, found here.
  • Chapter 6: Working with a single protein sequence (pp. 159-195 in second edition). Work through the following examples in this chapter using the entire HIV gp120 envelop protein sequence that you obtained from SWISS-PROT. We will then compare the results of these analyses with the actual structure of the gp120 protein obtained by X-ray crystallography.
    • ProtParam
    • Looking for transmembrane segments

HIV Structure Research Project

Today you will begin your HIV gp120 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 how the evolution of variation of the viral DNA sequence affects the different patient groups, you will look at how variations in the viral sequence affect the structure and, therefore, function of the virus. For this week's journal assignment, you must indicate the question that you will study for your project and which data you will use (patients, visits). Justify your selection of patients and visits.

Week 9

To answer your question, you will need to do the following:

  1. Convert your DNA sequences into protein sequences.
    • How will you do this?
    • How will you know that it was done correctly?
  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 Chapter 6 that you ran on the entire gp120 sequence are applicable to the V3 fragment you are working with now?
    • How are they applicable?
  4. Chapter 11 contains procedures to use for working with protein 3D structures. Find the section on "Predicting the Secondary Structure of a Protein Sequence" and perform this on both the entire gp120 sequence and on the V3 fragment that we are now working with. You will compare the predictions with the actual structures. Use this link to do the prediction, [1]
  5. Download the structure files for the papers we read in journal club from the NCBI Structure Database.
  6. 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.) Familiarize yourself with the software features (rendering and coloring) with both the gp120 peptide and ternary complex structures. 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 (poly)peptide structure.
    • Locate all the secondary structure elements. Do these match the predictions you made above?
    • Locate the V3 region and figure out which sequences from your alignment are present in the structures and which sequences are absent.
  7. 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.
  8. The journal club papers we read are quite old already for a fast-moving field. Using the Web of Science (or PubMed or Structure) databases, find at least one more recent publication that has a structure of gp120 (V3) in it and download the structure file to view. What additional information has been learned from this new paper?
  9. Your presentation for Week 10 will be formatted similarly to the previous HIV Evolution Project. In this case, you will want to work on creating structure figures that illustrate what result you are trying to show.
    • Your presentation will be 15 minutes long (approximately 15 slides, one per minute). Include:
      • Title slide
      • Outline slide
      • Background that led you to ask your research question
      • Your question
      • How you answered your question, method/results
      • Interpretation of your results; answer to your question
      • Discussion and interprettion of your results in light of the new paper you found.
    • Upload your slides to the OpenWetware wiki by the Week 9 journal assignment deadline. 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.

Week 10

  • Project presentations in class.
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