Jcowan4 Journal Week 11

Biological Terms

Intracellular

Transcriptomic

Extracellular

Methionine

Biosynthesis

B-galactosidase

Homocysteine

Oxidative

Glutathione

Substrate

Transduction

Outline

What is the main result presented in this paper?

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

What is the importance or significance of this work?

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

What were the limitations in previous studies that led them to perform this work?

There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

How did they treat the yeast cells (what experiment were they doing?)

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?

Strains:

• YNR055.1

• YPC722, YPC723, YPC724,

• BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

• BYT1, BYT2, BYT12

• W303-1A

• DBY746

(*The information regarding the if they were haploid or diploid wa not given)

What media did they grow them in? What temperature? What type of incubator? For how long?

• Grown in translucent potassium-free YNB media
• Temperature: 28 Celsius
• Incubator: N/A
• The times used were 0, 10, 20, 40, 60 and 120 minutes

What controls did they use?

Controls: wild-type strain BY4741, 50mM KCI added

How many replicates did they perform per treatment or timepoint?

4 Replicates per timepoint

What method did they use to prepare the RNA, label it and hybridize it to the microarray?

RNA extraction using the Ribo Pure™-Yeast kit

What mathematical/statistical method did they use to analyze the data?

They used GEPAS v3.1

Are the data publicly available for download? From which web site?

The data could be found at Society for Applied Microbiology

Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.

Table 1 shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

Table 2 shows a list of strains that were used.

Figure 1 shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. X = Timepoint Y = Genes

Figure 2 (A) shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. B is a graph that shows mRna concentration from the microarray X = mRna change Y = Genes. C shows the concentration of Met and Cys after the procedure. X = Timepoint Y = Genes (Met/Cys)

Figure 3 shows the oxidative stress response in genes due to potassium deprivation. A shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. B shows images of the genes responding to the procedure. Y = Time intervals. C shows the change in Glutanione level due to potassium starvation.

Figure 4 shows the effects of methylglyoxal production and treholse production from potassium starvation. A shows how the production of each is made. B shows the changes in expression X = Timepoint Y = Changes in expression (-fold). C shows the levels of methyglyoxal when affected by potassium starvation. X = Timepoint Y = Methyglyoxal Levels.

Figure 5 shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. A shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. B shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. C & D shows the graph depicting the relative concentration of intracellular ammonium after treatment.

Figure 6 shows expression of genes controlling cyclins express various responses to potassium starvation. A shows a graph demonstrating the change in expression levels of retrograde after potassium starvation. X = Timepoint Y = log2 change in expression levels. B are images depicting relative abundance of cyclin mRNA & C are images depicting relative abundance of cyclin protein

Figure 7 shows that potassium starvation decreases septin ring formation. A shows a graph that represents the change in expression levels of septin ring fomration genes after potassium starvation. B are images depicting the localization of Cdc11-GFP during treatment. C are images depicting relative abundance of Cdc11 protein. D are images depicting the localization of Cdc11 protein

How does this work compare with previous studies?

No other previous works.

What are the important implications of this work?

The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

What future directions should the authors take?

The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

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?

The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

Annotated Bibliography

• 1. Use a keyword search for the first three databases/tools and answer the following:
     • PubMed
       • What original keyword(s) did you use? How many results did you get?
       • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
     • Google Scholar
       • What original keyword(s) did you use? How many results did you get?
       • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
     • Web of Science
       • What original keyword(s) did you use? How many results did you get?
       • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
  2. Use the advanced search functions for each of these three databases/tools and answer the following:
     • PubMed
       • Which advanced search functions were most useful to narrow down the search? How many results did you get?
     • Google Scholar
       • Which advanced search functions were most useful to narrow down the search? How many results did you get?
     • Web of Science
       • Which advanced search functions were most useful to narrow down the search? How many results did you get?
     • Perform a prospective search on your article in the Web of Science and answer the following:
       • How many articles does this article cite?
       • How many articles cite this article?

Acknowledgements

This week we were put into teams. The team I was assigned to was Team Skinny Genes. The other members are Mihir Samdars, Aby Mesfin, David Ramirez, Christina Dominguez. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

References

Assignment	Individual Journal	Shared Journal
Week 1	jcowan4	Class Journal Week 1
Week 2	jcowan4 Journal Week 2	Class Journal Week 2
Week 3	FAS2 Week 3	Class Journal Week 3
Week 4	jcowan4 Journal Week 4	Class Journal Week 4
Week 5	iDog Week 5	Class Journal Week 5
Week 6	jcowan4 Journal Week 6	Class Journal Week 6
Week 7	jcowan4 Journal Week 7	Class Journal Week 7
Week 8	jcowan4 Journal Week 8	Class Journal Week 8
Week 9	jcowan4 Journal Week 9	Class Journal Week 9
Week 10	jcowan4 Journal Week 10	Class Journal Week 10
Week 11	jcowan4 Journal Week 11	Skinny Genes
Week 12/13	Skinny Genes Quality Assurance	Skinny Genes
Week 15	jcowan4 Journal Week 15	Class Journal Week 15

Misc. Links

• User:jcowan4

• Template:jcowan4

• Bio DB Home page

(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)