Jnimmers Week 6 - Revision history

Jnimmers: Invoke template

2019-10-10T02:43:45Z

Invoke template

Jnimmers: Bullet

2019-10-10T02:39:33Z

Bullet

Jnimmers: update acknowledgements

2019-10-10T02:38:54Z

update acknowledgements

Jnimmers: update acknowledgements

2019-10-10T02:38:10Z

update acknowledgements

Jnimmers: wording

2019-10-10T02:37:27Z

wording

Jnimmers: Answer Q 10

2019-10-10T02:37:07Z

Answer Q 10

Jnimmers: correctio

2019-10-10T02:28:40Z

correctio

Jnimmers: correction

2019-10-10T02:28:18Z

correction

Jnimmers: bullet

2019-10-10T02:22:01Z

bullet

Jnimmers: Bullet

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 ==Purpose==
 *The purpose of this assignment is learn about DNA assays, how they're carried out, their purpose and how to interpret the data collected from them.
 ==Questions==

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 ==Purpose==
-The purpose of this assignment is learn about DNA assays, how they're carried out, their purpose and how to interpret the data collected from them.
+*The purpose of this assignment is learn about DNA assays, how they're carried out, their purpose and how to interpret the data collected from them.
 [[Jnimmers Week 6 | Week 6 Individual Journal]]

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 ==Acknowledgements==
-*Thank you to [[User:Kdahlquist | Dr. Kam Dahlquist]] for her assistance in this class and for helping to teach us about the topics covered in this assignment.
+*Thank you to [[User:Kdahlquist | Dr. Kam Dahlquist]] for her assistance in this class and for helping to teach us about the topics covered in this assignment. Thank you for providing references necessary to answer these questions as well.
 *Thank you to my homework partner, [[User:Ymesfin | Yeabsira (Aby) Mesfin]] for his assitance on this assignment,. We met in person and spoke over the phone to coordinate questions and answers to the individual journal assignment questions.
 *Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

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 *Thank you to [[User:Kdahlquist | Dr. Kam Dahlquist]] for her assistance in this class and for helping to teach us about the topics covered in this assignment.
 *Thank you to my homework partner, [[User:Ymesfin | Yeabsira (Aby) Mesfin]] for his assitance on this assignment,. We met in person and spoke over the phone to coordinate questions and answers to the individual journal assignment questions.
 ==References==

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 ===10. (Question 16, p. 121) Using the microarray data, how could you verify that you had truly deleted TUP1 or overexpressed YAP1 in the experiments described in questions 8 and 9?===
-*These genes can be verified as being deleted (TUP1) or over expressed(Yap1p) by looking at the color of the spots corresponding to the genes that each gene is targeting. For example, because TUP1 is a known repressor linked to glucose levels, you would expect for target gene expression to be suppressed when the levels of glucose are depleted. If a green spot isn't seen in this case, it can only be concluded that the operating systm used to repress that gene in this particular situation is not doing it's function(TUP1 in this case), so it is either mutated to the point of non function, or simply deleted. The same can be said for YAP1: if a target gene of YAP1 is still being expressed with a depleted glucose storage, either the repressor is deleted, or the gene that allows for resistance to glucose level change is working ''too'' well, which calls for the gene's over expression.
+*These genes can be verified as being deleted (TUP1) or over expressed(Yap1p) by looking at the color of the spots corresponding to the genes that each gene is targeting. For example, because TUP1 is a known repressor linked to glucose levels, you would expect for target gene expression to be suppressed when the levels of glucose are depleted. If a green spot isn't seen in this case, it can only be concluded that the operating systm used to repress that gene in this particular situation is not doing it's function(TUP1 in this case), so it is either mutated to the point of non function, or simply deleted. The same can be said for YAP1: if a target gene of YAP1 is still being expressed with a depleted glucose storage, either the repressor is deleted, or the gene that allows for resistance to glucose level change is working ''too'' well, which indicated the gene's over expression.
 ==Acknowledgements==

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 ===9. (Question 14, p. 121) Consider a microarray experiment where cells that overexpress the transcription factor Yap1p were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented Yap1p target genes to be in the later time points of this experiment?===
-*The Yap1p target genes will likely show up as green due to an over expression of Yap1p means that the cell will likely be far more resistant to environmental stressors, allowing it to survive and freely express the Yap1p target genes even with low levels of glucose at later time points.
+*The Yap1p target genes will likely show up as red due to an over expression of Yap1p means that the cell will likely be far more resistant to environmental stressors, allowing it to survive and freely express the Yap1p target genes even with low levels of glucose at later time points.
 ===10. (Question 16, p. 121) Using the microarray data, how could you verify that you had truly deleted TUP1 or overexpressed YAP1 in the experiments described in questions 8 and 9?===

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 ===8. (Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later time points (glucose depleted) are labeled red. What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?===
-*I would expect to see a green spot at a later time point because, similar to the earlier experiment, the glucose repression would lead to the suppression of the the gene that was being tested on, however, with TUP1 being deleted, there is no gene that would have the job of repressing the genes that are supposed to be repressed, meaning that you would see a green spot, indicating that (due to lack of repression) the cells are still expressing those genes in the later time points. However, I believe that the cell would be in much worse shape, metabolically, because it cannot shut off its gene expression.
+*I would expect to see a red spot at a later time point because, similar to the earlier experiment, the glucose repression would lead to the suppression of the the gene that was being tested on, however, with TUP1 being deleted, there is no gene that would have the job of repressing the genes that are supposed to be repressed, meaning that you would see a green spot, indicating that (due to lack of repression) the cells are still expressing those genes in the later time points. However, I believe that the cell would be in much worse shape, metabolically, because it cannot shut off its gene expression.
 ===9. (Question 14, p. 121) Consider a microarray experiment where cells that overexpress the transcription factor Yap1p were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented Yap1p target genes to be in the later time points of this experiment?===