Mavila9 Week 12 Journal - Revision history

Mavila9: /* Article Outline */ conclusion

2019-11-14T08:53:22Z

‎Article Outline: conclusion

Mavila9: /* Conclusion */ conclusion

2019-11-14T08:18:50Z

‎Conclusion: conclusion

Mavila9: /* Purpose */

2019-11-14T08:06:12Z

‎Purpose

Mavila9: /* Purpose */

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‎Purpose

Mavila9: /* Purpose */

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‎Purpose

Mavila9: /* Files */ presentation

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‎Files: presentation

Mavila9 at 08:02, 14 November 2019

2019-11-14T08:02:38Z

Mavila9: /* Article Outline */ answers

2019-11-14T07:00:58Z

‎Article Outline: answers

Mavila9: /* Article Outline */ answers

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‎Article Outline: answers

Mavila9: /* Article Outline */

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‎Article Outline

@@ Line 47: / Line 47: @@
 #* The data is publicly available at the end of the paper on https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006
 # Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
-#* Figure 2A showed that within the first 30 minutes of exposure the pools of homocysteine, cystathionine, cysteine, gamma-glutamylcysteine, and GSH started to increase and continued to do so with time.
+#* Figure 2A-B shows that within the first 30 minutes of exposure the pools of homocysteine, cystathionine, cysteine, gamma-glutamylcysteine, and GSH started to increase and continued to do so with time.
-#**
+#** x-axis shows time in hours; y-axis shows intracellular sulfur metabolite concentrations in micromolar.
-#* What do the X and Y axes represent?
+#* Figure 3 shows sulfate utilization in cells exposed to 0.1 micromolar As(III) and 0.2 micromolar As(III).
-#* How were the measurements made?
+#** x-axis shows exposure to molarity of As(III); y-axis shows amount of 35S in proteins and GSH in amount of radioactivity (cpm).
-#* What trends are shown by the plots and what conclusions can you draw from the data?
+#* Figure 4A shows a heat map of gene expression after exposure to As(III).
-# How does this work compare with previous studies?
+#** x-axis shows amount of As(III) exposure in milimoles as well as time in hours; y-axis shows the gene beingobserved for expression changes; a third dimension shows upregulation or downregulation of gene expression.
 # What are the important implications of this work?
 # What future directions should the authors take?
 # Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed.  Are there any major flaws to the paper?
 ==Files==

@@ Line 62: / Line 62: @@
 ==Conclusion==
+In conclusion, this article demonstrated the how expression of several genes changed with exposure to As(III) and the role of Met4 and Yap1 presence on the changes of gene expression.
 ==References==

@@ Line 2: / Line 2: @@
 ==Purpose==
-The purpose of this project was to work as a team on [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 | primary literature] to demonstrate our understanding of microarray data analysis.
+The purpose of this project was to work as a team on [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 primary literature] to demonstrate our understanding of microarray data analysis.
 ==10 Words I Didn't Understand Before==

@@ Line 2: / Line 2: @@
 ==Purpose==
-The purpose of this project was to work as a team on [[https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 | primary literature]] to demonstrate our understanding of microarray data analysis.
+The purpose of this project was to work as a team on [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 | primary literature] to demonstrate our understanding of microarray data analysis.
 ==10 Words I Didn't Understand Before==

← Older revision		Revision as of 08:05, 14 November 2019
Line 2:		Line 2:

	==Purpose==		==Purpose==
		+	The purpose of this project was to work as a team on [[https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 \| primary literature]] to demonstrate our understanding of microarray data analysis.

	==10 Words I Didn't Understand Before==		==10 Words I Didn't Understand Before==

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 ==Files==
-[[media:Sulfinights presentation mavila9.pptx]]
+[[media:Sulfinights presentation mavila9.pptx | Sulfinights presentation mavila9]]
 ==Conclusion==

@@ Line 39: / Line 39: @@
 #* The amount of replicates per treatment was not mentioned in the article.
 # What method did they use to prepare the RNA, label it and hybridize it to the microarray?
-#* The RNA was hybridized with 32P-labeled PCR fragments of ''MET3'', ''MET25'', and ''MET14''.
+#* The RNA was isolated, then 20 micrograms of RNA was primed with 3 micrograms of random hexamer and 3 micrograms of anchored oligo(dT)20 primer. Next the RNA was labeled using a reverse transcription reaction with Cy3-dUTP or Cy5-dUTP in 30 microliters. The RNA was then hybridized with 32P-labeled PCR fragments of ''MET3'', ''MET25'', and ''MET14''.
 # What mathematical/statistical method did they use to analyze the data?
 # Are the data publicly available for download?  From which web site?
 # Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
 #* What do the X and Y axes represent?
 #* How were the measurements made?

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 #* This paper's main result was that cells responded to cellular arsenite acquisition by stimulating sulfur assimilation or glutathione biosynthesis pathways through the control of transcription factors Yap1p and Met4p. These results are found by transcriptome, proteome, and sulfur metabolite profiling of ''Saccharomyces cerevisiae's'' response to arsenite.
 # What is the importance or significance of this work?
-#*
+#* This work provides further information about the impact of arsenite on the environmental and human health. Due to its causative and curative properties for disease a more full understanding of global and specific responses can help development of medical therapies.
 # What were the limitations in previous studies that led them to perform this work?
 # How did they treat the yeast cells (what experiment were they doing?)
 # What strain(s) of yeast did they use?  Were the strain(s) haploid or diploid?
-# What media did they grow them in?  What temperature?  What type of incubator?  For how long?
+#* The following yeast strains were used:
-# What controls did they use?
+#** W303-1A
 # How many replicates did they perform per treatment or timepoint?
-# What method did they use to prepare the RNA, label it and hybridize it to the microarray?
+#* The amount of replicates per treatment was not mentioned in the article.
 # What mathematical/statistical method did they use to analyze the data?
 # Are the data publicly available for download?  From which web site?
-#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
+# Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
 #* What do the X and Y axes represent?
 #* How were the measurements made?

@@ Line 16: / Line 16: @@
 ==Article Outline==
-#What is the main result presented in this paper?
+# What is the main result presented in this paper?
-#* This paper's main result was that cells exposed to arsenite channel a large portion of their assimilated sulfur into glutathione biosynthesis due to controls by Yap1p and Met4p. This
+#* This paper's main result was that cells responded to cellular arsenite acquisition by stimulating sulfur assimilation or glutathione biosynthesis pathways through the control of transcription factors Yap1p and Met4p. These results are found by transcriptome, proteome, and sulfur metabolite profiling of ''Saccharomyces cerevisiae's'' response to arsenite.
 ==Conclusion==