Ymesfin Week 11

10 Biological Terms

1. homogenization = the process to create a homogenous mixture of a material. (Biology Online, 2019)
2. cyclin = a category of proteins that regulate the cell division cycle of eukaryotes (Oxford Dictionary of Biochemistry and Molecular Biology, 2006)
3. septins = a category of cytoskeletal proteins associated with GTB Binding protein and creating filaments that are associated with membrane dynamics, vesicle trafficking, apoptosis, and cytoskeletal remodeling (A Dictionary of Biomedicine, 2010)
4. trehalose = a disaccharide consisting of 1-1 α-linkages between glucose molecules (Biology Online, 2019)
5. regulon = a system of two genes on different parts of a chromosome that are systematically regulated by the same regulator molecule [(The Dictionary of Cell and Molecular Biology, 2007)]
6. reporter gene = a gene that synthesizes an easily detectible protein and is also upstream of the gene of interest. Using such genes allows researchers to easily monitor which variable affect the expression of the target gene (The Dictionary of Cell and Molecular Biology, 2007)
7. chemostat = the process by which a bacterial culture is kept in its exponential growth phase by monitoring the concentrations of rate limiting nutrients, media, and cells (A Dictionary of Biomedicine, 2010)
8. b-galactosidase = an enzyme encoded by the lacZ gene in the lac operon responsible for the hydrolysis of beta-galactose from the terminal end of sugars (A Dictionary of Biomedicine, 2010)
9. recombinant = a portion of spliced DNA out of the strand by restriction enzymes and reintroduced to different regions by ligases (The Dictionary of Cell and Molecular Biology, 2007)
10. immunofluorescence = a biochemical method with which a an antibody is linked to a fluorochrome in order to visually detect the presence of a particular antigen (A Dictionary of Biomedicine, 2010)

Outline

What is the main result presented in this paper?

The main findings of this article was that short term deprivation of potassium changes the mRNA levels of Saccharomyces cerevisiae, changes sulfur metabolism, induces oxidative stress, adn triggers the retrograde pathway. A repression of genes involved in ribosome synthesis, translation, adn the cell cycle was also observed after the cells were deprived of potassium.

What is the importance or significance of this work?

Given that potassium is an important cation in the cellular functioning of life, the findings of this study support the possibility of other biochemical pathways that necessitate potassium.

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

While other studies have demonstrated the relationship between potassium concentrations and large cellular functions such as enzyme activation, other pathways and cellular functions that rely on the availability of potassium have not been explored

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

The yeast cells were transferred to YNB based growth medium that lacked potassium and ammonium, and performed a time course for 10min, 20min, 40min, 60min, and 120min. After doing so, they profiled the expression levels of the genes in the yeast.

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

Yeast strains YNR055.1, YPC722, YPC723, YPC724, BY4741, BYT1, BYT2, BYT12, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1, YNR055.1, YPC722, YPC723, YPC724, W303-1A, DBY746 were used in this study. Information regarding the ploidy of the yeast was not given.

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

The yeast were grown in translucent potassium-free YNB media at 28°C for 10min, 20min, 40min, 60min,and 120min. Information regarding the incubator was not provided.

What controls did they use?

The study used wild-type strain BY4741 cultured in Translucent media with 50mM KCl as a control.

How many replicates did they perform per treatment or timepoint?

Four replicates were performed per timepoint.

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

Ribo Pure™-Yeast kit was used to extract the RNA. No information was provided regarding how they labeled and hybridized it to the microarray.

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

GEPAS v3.1 was used to process the microarray data.

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

The data is publically available for downloard from Society for Applied Microbiology

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

Fig. 1: Microarray Analysis-The majority of the genes were induced 60-120min after the cells were transferred to potassium free media. X Axis-timepoints; Y Axis-genes

Fig. 2: The genes involved in the creation of MET and SAM that were induced by potassium deprivation were not induced in the trk1 adn trk2 cells.

• 2A: no axis; Gene Ontology Analysis
• 2B: X Axis-genes; Y Axis- log2 mRNA change
• 2C: X Axis- time (min); Y Axis- Met/Cys (microM)

Fig. 3: Potassium starvation induced genes associated with oxidative stress. Fig. 4: Fig. 5: Fig. 6: Fig. 7:

What are the important implications of this work?

The findings of this study demonstrate the relationship between potassium and cellular functions within yeast.

Acknowledgements

Professor: Dr. Dahlquist

Homework Partners: Christina Dominguez, Jonar Cowan, David Ramirez, and Mihir Samdarshi

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

References

Barreto, L., Canadell, D., Valverde‐Saubí, D., Casamayor, A., & Ariño, J. (2012). The short‐term response of yeast to potassium starvation. Environmental microbiology, 14(11), 3026-3042.

Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org/

Blackshaw, S. E., & Lackie, J. M. (2007). The Dictionary of Cell and Molecular biology. Amsterdam: Academic Press.

Lackie, J., & OCallaghan, C. (2010). A Dictionary of Biomedicine. Oxford: Oxford University Press.

LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11

Oxford University Press. (2006). Oxford dictionary of biochemistry and molecular biology. Oxford.

Main Page

Ymesfin

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Skinny Genes

Week 12

Week 13

Week 14

Week 15