Zrusso Biol 368 week 10
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HIV Structure Redux
Powerpoint containing images of mutation points in HIV structure of V3 loop can be found here
Intro to DNA Microarrays
- pg. 110 #5 - Media:Gene_Transcription_Level_Comparison_Russo.xls
- pg. 110 #6b - Black at 1 hour for all genes. At hour 3 all are red ranked Z to X to Y from darkest to brightest but all are still pretty dark because all are ~3x increase. At hour 5 X and Y are both back to black and Z is still dark red at a 2x increase. At hour 9 X is a dark green at ~6x decrease, Y is bright green at ~20x decrease, and Z is still sitting at dark red with ~2x increase.
- pg. 110 #7 - Genes X, Y, and Z showed a similar transcription response in the first three hours, however after that point transcription began to vary wildly.
- pg. 118 #9 - Early in the experiment, both the control and the variable cultures of yeast had plentiful glucose in their media, it was only towards the middle and end that the glucose ran out in the variable culture.
- pg. 118 #10 - TEF4 is being repressed in the variable culture with a reduction in glucose while maintaining normal expression in the control. This is due to the fact that it is an elongation factor that helps in translation and one of the results from the DeRisi paper is that translation and ribosomal activity plummets in glucose starved yeast cells.
- pg. 120 #11 - The TCA cycle is induced in the reduction of glucose, but in reverse. This allows the yeast cell to take whatever energy and leftover intermediate molecules and transform them into storage sugars. Basically the yeast cell was beginning to hoard food for a long drought.
- pg. 120 #12 - To induce or repress all the genes in a pathway, the organism could simply use the same promoting or silencing mechanism for all the genes, this way if the pathway needs to be controlled it only takes one switch instead of many.
- pg. 121 #13 - Well I assume you are referring for the spot that would code for TUP1, in which case it would be green because the gene would not be present in the variable culture so no red dye.
Journal Club Article & Microarray Data