BIOL368/F11:Week 10

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'''This journal entry is due on Wednesday, November 2 at midnight PDT''' ''(Tuesday night/Wednesday morning)''.  NOTE that the server records the time as Eastern Daylight Time (EDT).  Therefore, midnight will register as 03:00.
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'''This journal entry is due on Wednesday, November 9 at midnight PST''' ''(Tuesday night/Wednesday morning)''.  NOTE that Daylight Savings Time ends this weekend.  I believe that the server will be adjusted to reflect this and will change over to record the time as Eastern Standard Time (EDT).  Therefore, midnight will register as 03:00.
__NOTOC__
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== Individual Journal Assignment ==
== Individual Journal Assignment ==
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* 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).
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* Store this journal entry as "''username'' Week 10" (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.'''''
* 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 to your journal entry from your user page.
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** Don't forget to add the "BIOL368/F11" category to the end of your wiki page.
** Don't forget to add the "BIOL368/F11" category to the end of your wiki page.
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== Introduction to DNA Microarrays ==
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=== HIV Structure Redux ===
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=== Read ===   
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* Pick two amino acid substitutions (two different positions) that you found in your HIV Structure Project.  Use StarBiochem or Cn3D to locate those amino acids on the structure (either from Kwong or Stanfield).
 +
* Take a screenshot showing a view that shows the amino acid in question (one screenshot per amino acid).  Save your screenshot in a PowerPoint slide and use an arrow or circle to point to the amino acid.
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* Interpret whether the amino acid is on the surface, buried, or at an interface with another protein, and whether the substitution should affect the function.
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=== Introduction to DNA Microarrays ===
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==== Read ====   
* Brown, P.O. & Botstein, D. (1999) [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Exploring the new world of the genome with DNA microarrays] ''Nature Genetics''  21: 33-37.
* Brown, P.O. & Botstein, D. (1999) [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Exploring the new world of the genome with DNA microarrays] ''Nature Genetics''  21: 33-37.
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* DeRisi, J.L., Iyer, V.R., and Brown, P.O.  (1997)  [http://www.sciencemag.org/content/278/5338/680.full Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale.]  ''Science'' 278: 680-686.
* DeRisi, J.L., Iyer, V.R., and Brown, P.O.  (1997)  [http://www.sciencemag.org/content/278/5338/680.full Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale.]  ''Science'' 278: 680-686.
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=== Answer the following Discovery Questions from Chapter 4 ===
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==== Answer the following Discovery Questions from Chapter 4 ====
* Number 5 from p. 110:  Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time.
* Number 5 from p. 110:  Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time.
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* Number 16 from p. 121:  What types of control spots would you like to see in this type of experiment?  How could you verify that you had truly deleted or overexpressed a particular gene?
* Number 16 from p. 121:  What types of control spots would you like to see in this type of experiment?  How could you verify that you had truly deleted or overexpressed a particular gene?
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=== Finding a Journal Club Article/Microarray Dataset ===
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==== Finding a Journal Club Article/Microarray Dataset ====
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* Next week you will begin the DNA Microarray Project by preparing for your next Journal Club presentation that will take place in Week 12.  You may choose to work ahead towards this presentation by finding your Journal Club article and corresponding microarray dataset with which you will perform your project.  You will work in groups of 2 or 3 on this project.  Your task is to find a published microarray dataset that measures gene expression from one of the following species:
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* Next week you will begin the DNA Microarray Project by preparing for your next Journal Club presentation that will take place in Week 12.  You will work in groups of 2 or 3 on this project.  Groups are:
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** ''Saccharomyces cerevisiae'' (yeast)
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** Chris, Nicki - ''Mycobacterium smegmatis''
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** Isaiah, Sam
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** Alex, Bobby, Zeb - ''Staphylococcus aureus'' MRSA25  [[http://www.ebi.ac.uk/arrayexpress/experiments/E-BUGS-65 Staph Article]]
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* You may choose to work ahead towards this presentation by finding your Journal Club article and corresponding microarray dataset with which you will perform your project.  Your task is to find a published microarray dataset that measures gene expression from one of the following species:
** ''Escherichia coli'' K12
** ''Escherichia coli'' K12
** ''Helicobacter pylori''
** ''Helicobacter pylori''
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** ''Plasmodium falciparum''
** ''Plasmodium falciparum''
** ''Pseudomonas aerugenosa''
** ''Pseudomonas aerugenosa''
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** ''Saccharomyces cerevisiae'' (yeast)
** ''Salmonella typhimurium''
** ''Salmonella typhimurium''
** ''Staphylococcus aureus'' MRSA252
** ''Staphylococcus aureus'' MRSA252
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== Shared Journal Assignment ==
== Shared Journal Assignment ==
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* Store your journal entry in the shared [[BIOL368/F11:Class Journal Week 9]] page.  If this page does not exist yet, go ahead and create it.
+
* Store your journal entry in the shared [[BIOL368/F11:Class Journal Week 10]] 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 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.
* Link the shared journal page to this assignment page.
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=== Reflection ===
=== Reflection ===
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After reading the Brown & Botstein (1999), Campbell & Heyer (2003), and DeRisi et al. (1997) readings, reflect on the following:
# What was the purpose of these readings?
# What was the purpose of these readings?
# What did I learn from these readings?
# What did I learn from these readings?
# What did I not understand (yet) about the readings?
# What did I not understand (yet) about the readings?

Current revision

BIOL368: Bioinformatics Laboratory

Loyola Marymount University

Home       People        HIV Evolution       HIV Structure       DNA Microarrays       Lionshare       Help  

This journal entry is due on Wednesday, November 9 at midnight PST (Tuesday night/Wednesday morning). NOTE that Daylight Savings Time ends this weekend. I believe that the server will be adjusted to reflect this and will change over to record the time as Eastern Standard Time (EDT). Therefore, midnight will register as 03:00.


Individual Journal Assignment

  • Store this journal entry as "username Week 10" (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/F11" category to the end of your wiki page.

HIV Structure Redux

  • Pick two amino acid substitutions (two different positions) that you found in your HIV Structure Project. Use StarBiochem or Cn3D to locate those amino acids on the structure (either from Kwong or Stanfield).
  • Take a screenshot showing a view that shows the amino acid in question (one screenshot per amino acid). Save your screenshot in a PowerPoint slide and use an arrow or circle to point to the amino acid.
  • Interpret whether the amino acid is on the surface, buried, or at an interface with another protein, and whether the substitution should affect the function.

Introduction to DNA Microarrays

Read

Answer the following Discovery Questions from Chapter 4

  • Number 5 from p. 110: Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time.
  • Number 6b. from p. 110: Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes. These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen. Using the color scale from Figure 4.6, determine the color for each ratio in Figure 4.7b.
  • Number 7 from p. 110: Were any of the genes in Figure 4.7b transcribed similarly?
  • Number 9 from p. 118: Why would most spots be yellow at the first time point?
  • Number 10 p. 118 Go to http://www.yeastgenome.org and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4’s gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
  • Number 11 from p. 120: Why would TCA cycle genes be induced if the glucose supply is running out?
  • Number 12 from p. 120: What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
  • Number 13 from p. 121: Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?
  • Number 14 from p. 121: What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
  • Number 15 from p. 121: Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
  • Number 16 from p. 121: What types of control spots would you like to see in this type of experiment? How could you verify that you had truly deleted or overexpressed a particular gene?

Finding a Journal Club Article/Microarray Dataset

  • Next week you will begin the DNA Microarray Project by preparing for your next Journal Club presentation that will take place in Week 12. You will work in groups of 2 or 3 on this project. Groups are:
    • Chris, Nicki - Mycobacterium smegmatis
    • Isaiah, Sam
    • Alex, Bobby, Zeb - Staphylococcus aureus MRSA25 [Staph Article]
  • You may choose to work ahead towards this presentation by finding your Journal Club article and corresponding microarray dataset with which you will perform your project. Your task is to find a published microarray dataset that measures gene expression from one of the following species:
    • Escherichia coli K12
    • Helicobacter pylori
    • Mycobacterium smegmatis
    • Mycobacterium tuberculosis
    • Plasmodium falciparum
    • Pseudomonas aerugenosa
    • Saccharomyces cerevisiae (yeast)
    • Salmonella typhimurium
    • Staphylococcus aureus MRSA252
    • Vibrio cholerae
  • Microarray data is not centrally located on the web. Some major sources are:
  • All journal club articles/microarray datasets are subject to approval by the instructor.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F11:Class Journal Week 10 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/F11" category to the end of the wiki page (if someone has not already done so).

Reflection

After reading the Brown & Botstein (1999), Campbell & Heyer (2003), and DeRisi et al. (1997) readings, reflect on the following:

  1. What was the purpose of these readings?
  2. What did I learn from these readings?
  3. What did I not understand (yet) about the readings?
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