Jcowan4 Journal Week 11

Biological Terms

Intracellular: Occurring or being (situated) inside a cell or cells. (Biology Online, 2019)

Transcriptomic: The study of all RNA molecules in a cell. RNA is copied from pieces of DNA and contains information to make proteins and perform other important functions in the cell. Transcriptomics is used to learn more about how genes are turned on in different types of cells and how this may help cause certain diseases, such as cancer.

Extracellular: Occurring or being (situated) outside the cell or cells. (Biology Online, 2019)

Methionine: (Science: biochemistry) Contains the SCH3 group that can act as a methyl donor (see s adenosyl methionine). Common in proteins but at low frequency. The met x linkage is subject to specific cleavage by cyanogen bromide. (Biology Online, 2019)

Biosynthesis: The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes (to catalyze the reaction) and energy source (such as ATP). (Biology Online, 2019)

B-galactosidase: A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.

Homocysteine: The chemical reactions and pathways resulting in the formation of homocysteine, 2-amino-4-sulfanylbutanoic acid.

Oxidative: Capable of oxidizing other substances. Of, pertaining to, or produced by oxidation. (Biology Online, 2019)

Glutathione: (Science: biochemistry) The tripeptide _ glutamylcysteinylglycine. It contains an unusual peptide Linkage between the _ carboxyl group of the glutamate side chain and the amine group of cysteine. (Biology Online, 2019)

Substrate: A substratum or an underlying stratum. (Biology Online, 2019)

Transduction: there are a group of viruses called bacteriophages. These bacteriophages inject their viral dna into the host cell of bacteria. The viral dna then becomes incorporated into the chromosome of the bacterium. Thus the viral dna forms part of the bacterial chromosome and will be copied to all daughter cells. Though this viral dna will become active again at low frequency's. (Biology Online, 2019)

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? Yeast (283103), potassium (259156), potassium and yeast (3055)
       • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? Potassium starvation and yeast (66)
     • Google Scholar
       • What original keyword(s) did you use? How many results did you get? Yeast (3090000), potassium (4370000), potassium and yeast (1290000)
       • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? potassium starvation and yeast (41600)
     • Web of Science
       • What original keyword(s) did you use? How many results did you get? Yeast (272999), potassium (271094), potassium and yeast (2162)
       • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? Potassium starvation and yeast (60)
  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? The most useful included: Text availability, most recent, filtering out the older articles. It narrowed down my search to under 100 articles.
     • Google Scholar
       • Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions include: time intervals of when the articles were released/updated, date. The result changed from 21600 to 2100.
     • Web of Science
       • Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions included: Times cited, Usage count, date after (year). Results went from 60 to 11

REFERENCE 1

1. Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351. DOI: 10.1371/journal.pbio.0040351
2. https://www.ncbi.nlm.nih.gov/pubmed/17048990
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609136/
4. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040351
5. https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0040351&type=printable
6. Copyright: � 2006 Hess et al
7. Article is open to the public
8. Availibility: Online
9. Publisher: PLOS Biology
10. Earliest Publish Date: 2003
11. Peer-reviewed: Yes
12. https://journals.plos.org/plosbiology/s/editorial-board
13. Impact Factor: 8.386 (2018)
14. Primary Research article
15. https://ndownloader.figshare.com/files/471538

REFERENCE 2

1. Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17
2. https://www.ncbi.nlm.nih.gov/pubmed/29218312
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716641/
4. http://www.ijcep.org/index.php/ijcep/article/view/182
5. http://www.ijcep.org/index.php/ijcep/article/view/182/162
6. © 2017 International Journal of Clinical and Experimental Physiology
7. Open to the public
8. Availability: Online
9. Published by Wolters Kluwer - Medknow
10. Earliest Published Daye: 2014
11. Peer-Reviewed
12. http://www.ijcep.org/index.php/ijcep/about/editorialTeam
13. Impact Factor: 1.706 (2016)
14. Review Article
15. NA

• Reflect:
  1. What impact does the choice of keywords have on your results? The important keywords lone are too broad of a topic. You have to be as specific as possible
  2. What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)? Pubmed is very well-rounded. It has open access and is able to locate articles easily. the drawback, however, is the limited data it provides. Google Scholar is very accessible with very basic information and does not always provide a doi. Web of science is closed to the public but the filters and advanced search provides easy access. However, it is aa paid website in comparison to the other two.

Data/Files

Skinny Genes Presentation

Conclusion

This week, I learned how to reference sources and to look up information to confirm its viability. I also learned how to properly format a presentation.

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

1. LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
2. MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
3. Lagarias, J.C., Duanmu, D., Casero, D., Dent, R.M., Gallaher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R. (2013). "Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival". Proceedings of the National Academy of Sciences of the United States of America. 110 (9): 3621–3626. doi:10.1073/pnas.1222375110.
4. Douglas, L. M., Alvarez, F. J., McCreary, C., & Konopka, J. B. (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12.
5. Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
6. Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
7. Lackie, J. M. (Ed.). (2007). The dictionary of cell & molecular biology. Academic Press. Retrieved November 11, 2019 from http://ebookcentral.proquest.com/lib/lmu/detail.action?docID=311420.
8. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. Jan 2009;25(2):288-289. Retrieved November 11, 2019 from http://amigo.geneontology.org/amigo/
9. Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., ... & Fisk, D. G. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Research, 40(D1), D700-D705.

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