Robert W Arnold Week 10

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Contents

Electronic Lab Notebook 10

Robert W Arnold

Week 10 Assignment

Final Presentation

  • Working with both Zeb and Alex for the final project.
  • Chose to look at and research Staphylococcus aureus.
  • I found the microarray we will be using on this [article].
  • Article based on microarray data [here]

StarBiochem Pictures

  • Here are the StarBiochem pictures with V3 regions circled and mutations pointed out.

In-Class Work

  1. See paper.
  2. For Gene X, hour 1 was black, hour 3 was red, hour 5 was black, and hour 9 was green. For Gene Y, hour 1 was black, hour 3 was red, hour 5 was green, and hour 9 was green. For Gene Z, hour 1 was black, hour 3 was red, hour 5 was red, and hour 9 was red.
  3. Yes, some of the genes should some similarities in transcription. All of them had an initial increase in expression. However, after the first three hours, transcription varied between the three genes.
  4. Initially, the control and variable had a lot of glucose in the samples which neither induces or represses gene expression. It was only towards the end that the amount of glucose declined.
  5. The TEF4 had stable expression over the first half but then became increasingly repressed. One could assume that this decline in expression is due to a decline in available glucose. The cell slows to preserve the falling food supply.
  6. TCA cycle genes would be used to produce more energy for the cell in the absence of glucose. TCA prduces ATP and NADH from glycolysis left overs.
  7. The organism could use promoters or silencers to allow or restrict certain genes. These pathways couuld be controlled by the binding of a single unit to a transcription line.
  8. When TUP1 is deleted, the color would be green because no red dye would be in the sample.
  9. The spots will be red with the overexpression of Yap1p.
  10. Yes, the loss of a repressor or the overexpression of a transcription factor can result in the repression of a gene. Genes can be dependent on the presence or absence of other genes in order to be expressed.
  11. Control spots I think would be yellow. If a gene is deleted it shouldn't be in the chip and if it is overexpressed it should be red.

Links

Biol 368 Homepage

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