Msamdars Week 11
Contents
- 1 Purpose
- 2 Ten Definitions
- 3 Journal Article Outline
- 3.1 What is the main result presented in this paper?
- 3.2 What is the importance or significance of this work?
- 3.3 What were the limitations in previous studies that led them to perform this work?
- 3.4 How did they treat the yeast cells (what experiment were they doing?)
- 3.5 What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
- 3.6 What media did they grow them in? What temperature? What type of incubator? For how long?
- 3.7 What controls did they use?
- 3.8 How many replicates did they perform per treatment or timepoint?
- 3.9 What method did they use to prepare the RNA, label it and hybridize it to the microarray?
- 3.10 What mathematical/statistical method did they use to analyze the data?
- 3.11 Are the data publicly available for download? From which web site?
- 3.12 Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
- 3.13 How does this work compare with previous studies?
- 3.14 What are the important implications of this work?
- 3.15 What future directions should the authors take?
- 3.16 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?
- 4 Annotated Bibliography
- 5 Data & Files
- 6 Conclusion
- 7 Acknowledgments
- 8 Other Links
- 9 References
Purpose
This week in our assignment we will read and analyze a scientific article and be able to explain the results to others. Furthermore, we will also be working in our teams for the first time and learn to navigate the team's dynamics.
Ten Definitions
retrograde pathway - Signals that travel from plastids to nuclei in plants and eukaryotic algae, and from mitochondria to nuclei in other eukaryotes, and tend to send messages regarding stress and environmental sensing (Lagarias et al., 2013)
septin ring - Septins are GTP-binding proteins in most eukaryotic cells (except in plant cells) and can form a protein complex in the shape of nonpolar filaments, filament bundles, rings, or cages (Douglas et al., 2005)
trehalose - A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates (Biology Online, 2019)
immunoblot - (AKA Western Blot) A procedure in which proteins separated by electrophoresis in polyacrylamide gels are transferred (blotted) onto nitrocellulose or nylon membranes and identified by specific complexing with antibodies that are either pre-or post-tagged with a labelled secondary protein. (Biology Online, 2019)
triose phosphate - (AKA Glyceraldehyde phosphate) A phosphate ester of the 3-carbon sugar glyceraldehyde and has chemical formula: C3H7O6P (Biology Online, 2019)
chemostat - Apparatus for maintaining a bacterial population in the exponential phase of growth by regulating the input of a rate-limiting nutrient and the removal of medium and cells (Smith, 2000)
Cdc11 - One of a family of mitotic septins that aid in cell division by forming a ring structure at the septum (Biology Online, 2019)
RT-PCR - Reverse transcriptase polymerase chain reaction; reverse transcription PCR PCR in which the starting template is RNA, implying the need for an initial reverse transcriptase step to make a DNA template. Some thermostable polymerases have appreciable reverse transcriptase activity; however, it is more common to perform an explicit reverse transcription, inactivate the reverse transcriptase or purify the product, and proceed to a separate conventional PCR. Abbreviation ambiguous because also used sloppily for real-time PCR. (Lackie, 2007)
bud neck - The constriction between the mother cell and daughter cell (bud) in an organism that reproduces by budding.
isozyme - (AKA Isoenzyme) Enzymes that differ in amino acid sequence but catalyze the same chemical reaction. These enzymes usually display different kinetic parameters (i.e. different KM values), or different regulatory properties. The existence of isozymes permits the fine-tuning of metabolism to meet the particular needs of a given tissue or developmental stage (Biology Online, 2019)
Journal Article Outline
What is the main result presented in this paper?
The main result of the paper states that short-term potassium deprivation has an effect on the mRNA transcription rate of around a thousand genes. They see that in particular genes that control sulfur metabolism, trigger an oxidative response, and activate the retrograde pathway get affected. It also says that they observe a significant decrease in overall ribosome creation and translation, components like cyclins and protein kinases, and decrease in septin assembly.
What is the importance or significance of this work?
Given that a lack of potassium showed a significant decrease in gene expression of certain pathways, this opens up a new field of study to see how exactly the potassium cation regulates these pathways.
What were the limitations in previous studies that led them to perform this work?
This study had apparently never been done before. Thus, this study was necessitated to perform a complete transcriptomic analysis.
How did they treat the yeast cells (what experiment were they doing?)
The scientists grew the cells at 28C in translucent K+ free medium supplemented with KCl solution. Cells were then transferred to fresh media with KCl, or without K+. Samples of both were then taken at 20, 40, 60, and 120 min from four replicates.
What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
The strains used were BY4741, BYT1, BYT2, BYT12, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1, YNR055.1 YPC722 (5), YPC723, YPC724, W303-1A, DBY746. It was not told to us which ploidy each strain was. However, according to the SGD wiki, BY4741 is a haploid strain (Cherry et al., 2011).
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 supplemented with 50 mM KCl. They did not specify an incubator, but did say the yeast was grown until the culture reached an optical density of 0.8.
What controls did they use?
They extracted a control from four replicates from the media supplemented with 50 mM KCl at every timepoints of the experiment.
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?
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?
- What trends are shown by the plots and what conclusions can you draw from the data?
How does this work compare with previous studies?
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?
Annotated Bibliography
Data & Files
Conclusion
Acknowledgments
This week my team members are in Skinny Genes which is composed of Jonar Cowan, Aby Mesfin, David Ramirez, Christina Dominguez, & myself. We worked in and out of class together.
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Other Links
| Links | ||
|---|---|---|
| Mihir Samdarshi User Page | ||
| Assignment Pages | Personal Journal Entries | Shared Journal Entries |
| Week 1 | Journal Week 1 | Class Journal Week 1 |
| Week 2 | Journal Week 2 | Class Journal Week 2 |
| Week 3 | FAS2/YPL231W Week 3 | Class Journal Week 3 |
| Week 4 | Journal Week 4 | Class Journal Week 4 |
| Week 5 | Database - AmtDB | Class Journal Week 5 |
| Week 6 | Journal Week 6 | Class Journal Week 6 |
| Week 7 | Journal Week 7 | Class Journal Week 7 |
| Week 8 | Journal Week 8 | Class Journal Week 8 |
| Week 9 | Journal Week 9 | Class Journal Week 9 |
| Assignment Pages | Personal Journal Entries | |
| Week 10 | Journal Week 10 | |
| Week 11 | Journal Week 11 | |
| Week 12/13 | Journal Week 12/13 | |
| Team Project Links | ||
| Skinny Genes Team Page | ||
References
- LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
- MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
- 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.
- 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.
- Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
- Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
- 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.
- 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/
- 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.
